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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/lefse">Debian Med / lefse</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lefse/commit/9590ab80cef40ae65d05d49137bfd8b4b8a1ea28">9590ab80</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-06T11:07:43Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add header to patch
</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
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<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/lefse/commit/9590ab80cef40ae65d05d49137bfd8b4b8a1ea28#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/format_input.py b/format_input.py</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">index dd3d2e0..8873ecb 100755</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/format_input.py</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/format_input.py</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -55,7 +55,7 @@</span> def read_input_file(inp_file, CommonArea):</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: use 2to3 to port from python2 to python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936836</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2019-09-06</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Index: lefse/format_input.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lefse.orig/format_input.py 2019-09-06 12:01:19.030688896 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lefse/format_input.py 2019-09-06 12:01:19.010689029 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -55,7 +55,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> return CommonArea</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> </span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> def transpose(data):</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +16,7 @@ index dd3d2e0..8873ecb 100755</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> def read_params(args):</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> parser = argparse.ArgumentParser(description='LEfSe formatting modules')</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -170,24 +170,24 @@</span><span class="idiff left right"> def get_class_slices(data):</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -170,24 +170,24 @@</span></span>
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15
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> def numerical_values(feats,norm):</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> mm = []</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,7 +47,7 @@ index dd3d2e0..8873ecb 100755</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> feats[k] = [val*mul[i] for i,val in enumerate(v)]</span>
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43
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> if numpy.mean(feats[k]) and (numpy.std(feats[k])/numpy.mean(feats[k])) < 1e-10:</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> feats[k] = [ float(round(kv*1e6)/1e6) for kv in feats[k]]</span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span><span class="idiff left right"> def add_missing_levels(ff):</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span></span>
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46
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> clades2leaves[n].append( f )</span>
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47
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> else:</span>
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48
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> clades2leaves[n] = [f]</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +56,7 @@ index dd3d2e0..8873ecb 100755</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> if k and k not in ff:</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> ff[k] = [sum(a) for a in zip(*[[float(fn) for fn in ff[vv]] for vv in v])]</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> return ff</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="p">@@ -306,7 +306,7 @@</span><span class="idiff left right"> def biom_processing(inp_file):</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -306,7 +306,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> for IDMetadataEntry in CommonArea['abndData'].funcGetMetadataCopy()[IDMetadataName]: #* Loop on all the metadata values</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> IDMetadata.append(IDMetadataEntry)</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> ResolvedData.append(IDMetadata) #Add the IDMetadata with all its values to the resolved area</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +65,7 @@ index dd3d2e0..8873ecb 100755</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> if key != IDMetadataName:</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> MetadataEntry = list() #* Set it up</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> MetadataEntry.append(key) #* And post it to the area</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="p">@@ -358,7 +358,7 @@</span><span class="idiff left right"> def check_params_for_biom_case(params, CommonArea):</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -358,7 +358,7 @@</span></span>
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64
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> else:</span>
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65
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> FlagError = True</span>
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66
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> if FlagError == True: #* If the User passed an invalid class</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,7 +74,7 @@ index dd3d2e0..8873ecb 100755</td>
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69
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> params['class'] = 2</span>
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70
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> params['subclass'] = 3</span>
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71
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> return params</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="p">@@ -375,8 +375,8 @@</span><span class="idiff left right"> if __name__ == '__main__':</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -375,8 +375,8 @@</span></span>
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73
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> #*************************************************************</span>
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74
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> if params['input_file'].endswith('.biom'):</span>
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75
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> try:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +85,7 @@ index dd3d2e0..8873ecb 100755</td>
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80
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> except ImportError:</span>
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81
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> sys.stderr.write("************************************************************************************************************ \n")</span>
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82
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> sys.stderr.write("* Error: Breadcrumbs libraries not detected - required to process biom files - run abnormally terminated * \n")</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="p">@@ -403,16 +403,16 @@</span><span class="idiff left right"> if __name__ == '__main__':</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -403,16 +403,16 @@</span></span>
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84
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"> if not params['subclass'] is None: ncl += 1 </span>
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85
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> if not params['subject'] is None: ncl += 1 </span>
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86
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -101,7 +106,7 @@ index dd3d2e0..8873ecb 100755</td>
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101
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> # data.insert(0,first_line)</span>
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102
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> # data = remove_missing(data,params['missing_p'])</span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"> cls = {}</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="p">@@ -426,7 +426,7 @@</span><span class="idiff left right"> if __name__ == '__main__':</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="p">@@ -426,7 +426,7 @@</span></span>
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105
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"> </span>
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106
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"> cls['subclass'] = rename_same_subcl(cls['class'],cls['subclass'])</span>
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107
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"> # if 'subclass' in cls.keys(): cls = group_small_subclasses(cls,params['subcl_min_card'])</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,7 +115,7 @@ index dd3d2e0..8873ecb 100755</td>
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110
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> </span>
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111
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> feats = dict([(d[0],d[1:]) for d in data])</span>
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112
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> </span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="p">@@ -446,7 +446,7 @@</span><span class="idiff left right"> if __name__ == '__main__':</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="p">@@ -446,7 +446,7 @@</span></span>
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114
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> if 'class' in cls: outf.write( "\t".join(list(["class"])+list(cls['class'])) + "\n" )</span>
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115
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"> if 'subclass' in cls: outf.write( "\t".join(list(["subclass"])+list(cls['subclass'])) + "\n" )</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"> if 'subject' in cls: outf.write( "\t".join(list(["subject"])+list(cls['subject'])) + "\n" )</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,11 +124,11 @@ index dd3d2e0..8873ecb 100755</td>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="diff"> </span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="diff"> with open(params['output_file'], 'wb') as back_file:</span>
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121
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"> pickle.dump(out,back_file) </span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/lefse.py b</span>/lefse.py</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index 0a29be0..75fc246 100755</span></span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/lefse.py</span></span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/lefse.py</span></span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="p">@@ -17,14 +17,14 @@</span><span class="idiff left right"> def init():</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/lefse.py</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/lefse.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/lefse.py 2019-09-06 12:01:19.010689029 +0100</span></span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="p">@@ -17,14 +17,14 @@</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"> def get_class_means(class_sl,feats):</span>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> means = {}</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,7 +146,7 @@ index 0a29be0..75fc246 100755</td>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="diff"> out.write(k+"\t"+str(math.log(max(max(v),1.0),10.0))+"\t")</span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="diff"> if k in res['lda_res_th']:</span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="diff"> for i,vv in enumerate(v):</span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="p">@@ -64,7 +64,7 @@</span><span class="idiff left right"> def test_rep_wilcoxon_r(sl,cl_hie,feats,th,multiclass_strat,mul_cor,fn,min_c,com</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="p">@@ -64,7 +64,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="diff"> tot_ok = 0</span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="diff"> alpha_mtc = th</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="diff"> all_diff = []</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -150,7 +155,7 @@ index 0a29be0..75fc246 100755</td>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"> dir_cmp = "not_set" #</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="diff"> l_subcl1, l_subcl2 = (len(cl_hie[pair[0]]), len(cl_hie[pair[1]]))</span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="diff"> if mul_cor != 0: alpha_mtc = th*l_subcl1*l_subcl2 if mul_cor == 2 else 1.0-math.pow(1.0-th,l_subcl1*l_subcl2)</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="p">@@ -120,8 +120,8 @@</span><span class="idiff left right"> def test_rep_wilcoxon_r(sl,cl_hie,feats,th,multiclass_strat,mul_cor,fn,min_c,com</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="p">@@ -120,8 +120,8 @@</span></span>
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154
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> if not diff and multiclass_strat: return False</span>
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155
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"> if diff and not multiclass_strat: all_diff.append(pair)</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"> if not multiclass_strat:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,7 +166,7 @@ index 0a29be0..75fc246 100755</td>
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161
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"> nk = 0</span>
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162
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="diff"> for a in all_diff:</span>
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163
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="diff"> if k in a: nk += 1</span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="p">@@ -132,7 +132,7 @@</span><span class="idiff left right"> def test_rep_wilcoxon_r(sl,cl_hie,feats,th,multiclass_strat,mul_cor,fn,min_c,com</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="p">@@ -132,7 +132,7 @@</span></span>
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165
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="diff"> </span>
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166
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="diff"> </span>
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167
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="diff"> def contast_within_classes_or_few_per_class(feats,inds,min_cl,ncl):</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -170,7 +175,7 @@ index 0a29be0..75fc246 100755</td>
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170
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="diff"> cols = [ff[i] for i in inds]</span>
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171
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="diff"> cls = [feats['class'][i] for i in inds]</span>
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172
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="diff"> if len(set(cls)) < ncl:</span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="p">@@ -147,8 +147,8 @@</span><span class="idiff left right"> def contast_within_classes_or_few_per_class(feats,inds,min_cl,ncl):</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="p">@@ -147,8 +147,8 @@</span></span>
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174
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="diff"> return False </span>
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175
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="diff"> def test_lda_r(cls,feats,cl_sl,boots,fract_sample,lda_th,tol_min,nlogs):</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -181,7 +186,7 @@ index 0a29be0..75fc246 100755</td>
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181
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="diff"> feats['class'] = list(cls['class'])</span>
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182
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="diff"> clss = list(set(feats['class']))</span>
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183
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="diff"> for uu,k in enumerate(fk):</span>
</pre>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="p">@@ -160,7 +160,7 @@</span><span class="idiff left right"> def test_lda_r(cls,feats,cl_sl,boots,fract_sample,lda_th,tol_min,nlogs):</span></span>
</pre>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="p">@@ -160,7 +160,7 @@</span></span>
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185
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="diff"> if feats['class'][i] == c:</span>
</pre>
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186
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="diff"> feats[k][i] = math.fabs(feats[k][i] + lrand.normalvariate(0.0,max(feats[k][i]*0.05,0.01)))</span>
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187
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="diff"> rdict = {}</span>
</pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -190,7 +195,7 @@ index 0a29be0..75fc246 100755</td>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="diff"> if a == 'class' or a == 'subclass' or a == 'subject':</span>
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191
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="diff"> rdict[a] = robjects.StrVector(b)</span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="diff"> else: rdict[a] = robjects.FloatVector(b)</span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="p">@@ -210,7 +210,7 @@</span><span class="idiff left right"> def test_lda_r(cls,feats,cl_sl,boots,fract_sample,lda_th,tol_min,nlogs):</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="p">@@ -210,7 +210,7 @@</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="diff"> for k in fk:</span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="diff"> m = max([numpy.mean([means[k][kk][p] for kk in range(boots)]) for p in range(len(pairs))])</span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="diff"> res[k] = math.copysign(1.0,m)*math.log(1.0+math.fabs(m),10)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -199,10 +204,10 @@ index 0a29be0..75fc246 100755</td>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="diff"> def test_svm(cls,feats,cl_sl,boots,fract_sample,lda_th,tol_min,nsvm):</span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/lefse2circlader.py b</span>/lefse2circlader.py</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index 79cc2a0..db01218 100755</span></span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/lefse2circlader.py</span></span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/lefse2circlader.py</span></span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/lefse2circlader.py</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/lefse2circlader.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/lefse2circlader.py 2019-09-06 12:01:19.010689029 +0100</span></span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="diff"> #!/usr/bin/env python</span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -211,11 +216,11 @@ index 79cc2a0..db01218 100755</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="diff"> </span>
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="diff"> import sys</span>
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/lefsebiom/AbundanceTable.py b</span>/lefsebiom/AbundanceTable.py</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index 77c11aa..349af50 100755</span></span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/lefsebiom/AbundanceTable.py</span></span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/lefsebiom/AbundanceTable.py</span></span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="p">@@ -4,24 +4,24 @@</span><span class="idiff left right"> Description: Class to abstract an abundance table and methods to run on such a t</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/lefsebiom/AbundanceTable.py</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/lefsebiom/AbundanceTable.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/lefsebiom/AbundanceTable.py 2019-09-06 12:01:19.018688976 +0100</span></span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="p">@@ -4,24 +4,24 @@</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="diff"> """</span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="diff"> #####################################################################################</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -255,7 +260,7 @@ index 77c11aa..349af50 100755</td>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="diff"> #####################################################################################</span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="diff"> __author__ = "Timothy Tickle"</span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"><span class="p">@@ -35,8 +35,8 @@</span><span class="idiff left right"> __status__ = "Development"</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="p">@@ -35,8 +35,8 @@</span></span>
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259
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="diff"> import csv</span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="diff"> import sys</span>
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="diff"> import blist</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -266,7 +271,7 @@ index 77c11aa..349af50 100755</td>
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="diff"> import copy</span>
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="diff"> from datetime import date</span>
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="p">@@ -44,690 +44,731 @@</span><span class="idiff left right"> import os</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="p">@@ -44,690 +44,731 @@</span></span>
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270
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="diff"> import re</span>
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="diff"> import scipy.stats</span>
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="diff"> import string</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -523,13 +528,61 @@ index 77c11aa..349af50 100755</td>
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The original number of features in the table</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._iOriginalFeatureCount = -1</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Represents an abundance table and contains common function to perform on the object.</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The name of the object relating to the file it was read from or would have been read from if it exists</span></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Keeps tract of changes to the file through the name</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Will be used to write out the object to a file as needed</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._strOriginalName = strName</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The original number of samples in the table</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._iOriginalSampleCount = -1</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Data sparsity type</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.fSparseMatrix = dictFileMetadata.get(ConstantsBreadCrumbs.c_strSparsityKey,False) if dictFileMetadata else False</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Data metadata</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The column (sample) metdata</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._dictTableMetadata = dictMetadata</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The row (feature) metadata (Row Metadata object)</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.rwmtRowMetadata = rwmtRowMetadata</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Represents an abundance table and contains common function to perform on the object.</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Data</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The abundance data</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._npaFeatureAbundance = npaAbundance</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Logistical</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Clade prefixes for biological samples</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._lsCladePrefixes = ["k__","p__","c__","o__","f__","g__","s__"]</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #This is not a hashable object</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.__hash__ = None</span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Prep the object</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._fIsNormalized = self._fIsSummed = None</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #If contents is not a false then set contents to appropriate objects</span></span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Checking to see if the data is normalized, summed and if we need to run a filter on it.</span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( self._npaFeatureAbundance != None ) and self._dictTableMetadata:</span></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._iOriginalFeatureCount = self._npaFeatureAbundance.shape[0]</span></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._iOriginalSampleCount = len(self.funcGetSampleNames())</span></span>
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._fIsNormalized = ( max( [max( list(a)[1:] or [0] ) for a in self._npaFeatureAbundance] or [0] ) <= 1 )</span></span>
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lsLeaves = AbundanceTable.funcGetTerminalNodesFromList( [a[0] for a in self._npaFeatureAbundance], self._cFeatureDelimiter )</span></span>
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._fIsSummed = ( len( lsLeaves ) != len( self._npaFeatureAbundance ) )</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Occurence filtering</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Removes features that do not have a given level iLowestAbundance in a given amount of samples iLowestSampleOccurence</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( not self._fIsNormalized ) and lOccurenceFilter:</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- iLowestAbundance, iLowestSampleOccurrence = lOccurenceFilter</span></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.funcFilterAbundanceBySequenceOccurence( iLowestAbundance, iLowestSampleOccurrence )</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ This class is made from an abundance data file. What is expected is a text file delimited by</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ a character (which is given to the object). The first column is expected to be the id column</span></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for each of the rows. Metadata is expected before measurement data. Columns are samples and</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -537,15 +590,11 @@ index 77c11aa..349af50 100755</td>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ This object is currently not hashable.</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The original number of samples in the table</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._iOriginalSampleCount = -1</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __init__(self, npaAbundance, dictMetadata, strName, strLastMetadata, rwmtRowMetadata=None, dictFileMetadata=None, lOccurenceFilter=None, cFileDelimiter=ConstantsBreadCrumbs.c_cTab, cFeatureNameDelimiter="|"):</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Constructor for an abundance table.</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Data sparsity type</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.fSparseMatrix = dictFileMetadata.get(ConstantsBreadCrumbs.c_strSparsityKey,False) if dictFileMetadata else False</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ :param npaAbundance: Structured Array of abundance data (Row=Features, Columns=Samples)</span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ :type: Numpy Structured Array abundance data (Row=Features, Columns=Samples)</span></span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ :param dictMetadata: Dictionary of metadata {"String ID":["strValue","strValue","strValue","strValue","strValue"]}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -651,51 +700,11 @@ index 77c11aa..349af50 100755</td>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._fIsNormalized = (</span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ max([max(list(a)[1:] or [0]) for a in self._npaFeatureAbundance] or [0]) <= 1)</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Data metadata</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The column (sample) metdata</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._dictTableMetadata = dictMetadata</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ lsLeaves = AbundanceTable.funcGetTerminalNodesFromList(</span></span>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [a[0] for a in self._npaFeatureAbundance], self._cFeatureDelimiter)</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._fIsSummed = (len(lsLeaves) != len(self._npaFeatureAbundance))</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The row (feature) metadata (Row Metadata object)</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.rwmtRowMetadata = rwmtRowMetadata</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Data</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #The abundance data</span></span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._npaFeatureAbundance = npaAbundance</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Logistical</span></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Clade prefixes for biological samples</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._lsCladePrefixes = ["k__","p__","c__","o__","f__","g__","s__"]</span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #This is not a hashable object</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.__hash__ = None</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ### Prep the object</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._fIsNormalized = self._fIsSummed = None</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #If contents is not a false then set contents to appropriate objects</span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Checking to see if the data is normalized, summed and if we need to run a filter on it.</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( self._npaFeatureAbundance != None ) and self._dictTableMetadata:</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._iOriginalFeatureCount = self._npaFeatureAbundance.shape[0]</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._iOriginalSampleCount = len(self.funcGetSampleNames())</span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._fIsNormalized = ( max( [max( list(a)[1:] or [0] ) for a in self._npaFeatureAbundance] or [0] ) <= 1 )</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lsLeaves = AbundanceTable.funcGetTerminalNodesFromList( [a[0] for a in self._npaFeatureAbundance], self._cFeatureDelimiter )</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._fIsSummed = ( len( lsLeaves ) != len( self._npaFeatureAbundance ) )</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Occurence filtering</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Removes features that do not have a given level iLowestAbundance in a given amount of samples iLowestSampleOccurence</span></span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( not self._fIsNormalized ) and lOccurenceFilter:</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- iLowestAbundance, iLowestSampleOccurrence = lOccurenceFilter</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.funcFilterAbundanceBySequenceOccurence( iLowestAbundance, iLowestSampleOccurrence )</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Occurence filtering</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Removes features that do not have a given level iLowestAbundance in a given amount of samples iLowestSampleOccurence</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (not self._fIsNormalized) and lOccurenceFilter:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1418,7 +1427,8 @@ index 77c11aa..349af50 100755</td>
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1418
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1427
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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="diff"> + The last dict is a collection of BIOM fielparameters when converting from a BIOM file</span>
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1419
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1428
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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="diff"> + [Numpy structured Array, Dictionary, Numpy structured array, dict]</span>
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1420
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1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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1421
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="diff"> </span>
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1422
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1432
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<pre style="margin: 0;"> <span id="LC1432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Open file from a stream or file path</span></span>
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1423
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1433
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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- istmInput = open( xInputFile, 'rU' ) if isinstance(xInputFile, str) else xInputFile</span></span>
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1424
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1434
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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Flag that when incremented will switch from metadata parsing to data parsing</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1529,8 +1539,6 @@ index 77c11aa..349af50 100755</td>
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1529
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1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ConstantsBreadCrumbs.c_strTypekey:ConstantsBreadCrumbs.c_strDefaultPCLFileTpe,</span></span>
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1530
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1540
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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ConstantsBreadCrumbs.c_strURLKey:ConstantsBreadCrumbs.c_strDefaultPCLURL,</span></span>
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1531
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1541
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ConstantsBreadCrumbs.c_strSparsityKey:ConstantsBreadCrumbs. c_fDefaultPCLSparsity}]</span></span>
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1532
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<pre style="margin: 0;">-<span id="LC1532" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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1533
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<pre style="margin: 0;">-<span id="LC1533" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1534
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1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Open file from a stream or file path</span></span>
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1535
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1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ istmInput = open(xInputFile, 'rU') if isinstance(</span></span>
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1536
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1544
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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ xInputFile, str) else xInputFile</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1654,7 +1662,7 @@ index 77c11aa..349af50 100755</td>
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1654
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1662
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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="diff"> </span>
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1655
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1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="diff"> # def funcAdd(self,abndTwo,strFileName=None):</span>
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1656
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1664
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="diff"> # """</span>
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1657
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<pre style="margin: 0;">-<span id="LC1657" class="line" lang="diff"><span class="p">@@ -769,7 +810,7 @@</span><span class="idiff left right"> class AbundanceTable:</span></span>
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1665
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<pre style="margin: 0;">+<span id="LC1665" class="line" lang="diff"><span class="p">@@ -769,7 +810,7 @@</span></span>
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1658
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="diff"> # lsFeaturesCombined = list(set(lsFeatures1+lsFeature2))</span>
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1667
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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="diff"> #</span>
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1660
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1668
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<pre style="margin: 0;"> <span id="LC1668" class="line" lang="diff"> # #Add samples by features (Use 0.0 for empty data features, use NA for empty metadata features)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1663,7 +1671,7 @@ index 77c11aa..349af50 100755</td>
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1671
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<pre style="margin: 0;"> <span id="LC1671" class="line" lang="diff"> #</span>
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1664
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1672
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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="diff"> # #Combine metadata</span>
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1665
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1673
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<pre style="margin: 0;"> <span id="LC1673" class="line" lang="diff"> # dictMetadata1 = self.funcGetMetadataCopy()</span>
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1666
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<pre style="margin: 0;">-<span id="LC1666" class="line" lang="diff"><span class="p">@@ -797,1660 +838,1753 @@</span><span class="idiff left right"> class AbundanceTable:</span></span>
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1674
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<pre style="margin: 0;">+<span id="LC1674" class="line" lang="diff"><span class="p">@@ -797,1660 +838,1753 @@</span></span>
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1675
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<pre style="margin: 0;"> <span id="LC1675" class="line" lang="diff"> # strLastMetadata = self.funcGetLastMetadataName(),</span>
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1676
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<pre style="margin: 0;"> <span id="LC1676" class="line" lang="diff"> # cFileDelimiter = self.funcGetFileDelimiter(), cFeatureNameDelimiter=self.funcGetFeatureDelimiter())</span>
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1669
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1677
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<pre style="margin: 0;"> <span id="LC1677" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5074,11 +5082,11 @@ index 77c11aa..349af50 100755</td>
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5082
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<pre style="margin: 0;"> <span id="LC5082" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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5075
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5083
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<pre style="margin: 0;"> <span id="LC5083" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ BiomCommonArea[ConstantsBreadCrumbs.c_BiomFileInfo][strInsertKey] = PostBiomValue</span></span>
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5076
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5084
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<pre style="margin: 0;"> <span id="LC5084" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return BiomCommonArea</span></span>
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<pre style="margin: 0;">-<span id="LC5077" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/lefsebiom/CClade.py b</span>/lefsebiom/CClade.py</span></span>
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5078
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<pre style="margin: 0;">-<span id="LC5078" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index 5bd1c44..48e7031 100644</span></span></span>
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5079
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<pre style="margin: 0;">-<span id="LC5079" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/lefsebiom/CClade.py</span></span></span>
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5080
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<pre style="margin: 0;">-<span id="LC5080" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/lefsebiom/CClade.py</span></span></span>
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5081
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<pre style="margin: 0;">-<span id="LC5081" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span><span class="idiff left right"> class CClade:</span></span>
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5085
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<pre style="margin: 0;">+<span id="LC5085" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/lefsebiom/CClade.py</span></span>
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<pre style="margin: 0;">+<span id="LC5086" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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5087
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<pre style="margin: 0;">+<span id="LC5087" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/lefsebiom/CClade.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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5088
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<pre style="margin: 0;">+<span id="LC5088" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/lefsebiom/CClade.py 2019-09-06 12:01:19.018688976 +0100</span></span></span>
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<pre style="margin: 0;">+<span id="LC5089" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span></span>
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5082
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5090
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<pre style="margin: 0;"> <span id="LC5090" class="line" lang="diff"> #Then take a copy of the child's</span>
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5083
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5091
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<pre style="margin: 0;"> <span id="LC5091" class="line" lang="diff"> #If they now have a copy of a child's but have other children</span>
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5084
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5092
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<pre style="margin: 0;"> <span id="LC5092" class="line" lang="diff"> #Sum their children with thier current values</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5087,7 +5095,7 @@ index 5bd1c44..48e7031 100644</td>
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5087
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5095
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<pre style="margin: 0;"> <span id="LC5095" class="line" lang="diff"> adChild = pChild.impute( )</span>
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5088
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5096
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<pre style="margin: 0;"> <span id="LC5096" class="line" lang="diff"> if self.m_adValues:</span>
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5089
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5097
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<pre style="margin: 0;"> <span id="LC5097" class="line" lang="diff"> for i in range( len( adChild or [] ) ):</span>
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5090
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<pre style="margin: 0;">-<span id="LC5090" class="line" lang="diff"><span class="p">@@ -118,7 +118,7 @@</span><span class="idiff left right"> class CClade:</span></span>
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5098
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<pre style="margin: 0;">+<span id="LC5098" class="line" lang="diff"><span class="p">@@ -118,7 +118,7 @@</span></span>
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5091
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5099
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<pre style="margin: 0;"> <span id="LC5099" class="line" lang="diff"> #Union all the results from freeze of all children</span>
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5092
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5100
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<pre style="margin: 0;"> <span id="LC5100" class="line" lang="diff"> #Call freeze but append the child clade to the clade in the call.</span>
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5093
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5101
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<pre style="margin: 0;"> <span id="LC5101" class="line" lang="diff"> #And give an incremented depth</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5096,7 +5104,7 @@ index 5bd1c44..48e7031 100644</td>
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5096
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5104
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<pre style="margin: 0;"> <span id="LC5104" class="line" lang="diff"> setiRet |= pChild._freeze( hashValues, iTarget, astrClade + [strChild], iDepth, fLeaves )</span>
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5097
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5105
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<pre style="margin: 0;"> <span id="LC5105" class="line" lang="diff"> setiRet = set( ( i + 1 ) for i in setiRet )</span>
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5098
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<td class="diff-line-num new_line" data-linenumber="5106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5106
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<pre style="margin: 0;"> <span id="LC5106" class="line" lang="diff"> else:</span>
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5099
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<td class="diff-line-num new_line old" data-linenumber="5107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5099" class="line" lang="diff"><span class="p">@@ -155,7 +155,7 @@</span><span class="idiff left right"> class CClade:</span></span>
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5107
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<pre style="margin: 0;">+<span id="LC5107" class="line" lang="diff"><span class="p">@@ -155,7 +155,7 @@</span></span>
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5100
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5108
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<pre style="margin: 0;"> <span id="LC5108" class="line" lang="diff"> if self.m_hashChildren:</span>
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5101
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5109
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<pre style="margin: 0;"> <span id="LC5109" class="line" lang="diff"> strRet += " "</span>
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5102
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5110
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<pre style="margin: 0;"> <span id="LC5110" class="line" lang="diff"> if self.m_hashChildren:</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5105,11 +5113,11 @@ index 5bd1c44..48e7031 100644</td>
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5105
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5113
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<pre style="margin: 0;"> <span id="LC5113" class="line" lang="diff"> </span>
</pre>
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5106
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5114
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<pre style="margin: 0;"> <span id="LC5114" class="line" lang="diff"> return ( strRet + ">" )</span>
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5107
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5115
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<pre style="margin: 0;"> <span id="LC5115" class="line" lang="diff"> </span>
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5108
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<pre style="margin: 0;">-<span id="LC5108" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/lefsebiom/ValidateData.py b</span>/lefsebiom/ValidateData.py</span></span>
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5109
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<pre style="margin: 0;">-<span id="LC5109" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index 5943240..d95222f 100755</span></span></span>
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5110
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<pre style="margin: 0;">-<span id="LC5110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/lefsebiom/ValidateData.py</span></span></span>
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5111
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<pre style="margin: 0;">-<span id="LC5111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/lefsebiom/ValidateData.py</span></span></span>
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5112
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<pre style="margin: 0;">-<span id="LC5112" class="line" lang="diff"><span class="p">@@ -449,7 +449,7 @@</span><span class="idiff left right"> class ValidateData:</span></span>
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5116
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<pre style="margin: 0;">+<span id="LC5116" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/lefsebiom/ValidateData.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5117
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<pre style="margin: 0;">+<span id="LC5117" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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5118
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<pre style="margin: 0;">+<span id="LC5118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/lefsebiom/ValidateData.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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5119
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<pre style="margin: 0;">+<span id="LC5119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/lefsebiom/ValidateData.py 2019-09-06 12:01:19.018688976 +0100</span></span></span>
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5120
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<pre style="margin: 0;">+<span id="LC5120" class="line" lang="diff"><span class="p">@@ -449,7 +449,7 @@</span></span>
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5113
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5121
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<pre style="margin: 0;"> <span id="LC5121" class="line" lang="diff"> </span>
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5114
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<td class="diff-line-num new_line" data-linenumber="5122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5122
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<pre style="margin: 0;"> <span id="LC5122" class="line" lang="diff"> #Check elements</span>
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5115
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5123
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<pre style="margin: 0;"> <span id="LC5123" class="line" lang="diff"> listSize = len(parameterValue)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5118,7 +5126,7 @@ index 5943240..d95222f 100755</td>
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5118
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5126
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<pre style="margin: 0;"> <span id="LC5126" class="line" lang="diff"> if(not ValidateData.funcIsValidNumeric(parameterValue[i])):</span>
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5119
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5127
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<pre style="margin: 0;"> <span id="LC5127" class="line" lang="diff"> return False</span>
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5120
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5128
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<pre style="margin: 0;"> <span id="LC5128" class="line" lang="diff"> return True</span>
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5121
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<pre style="margin: 0;">-<span id="LC5121" class="line" lang="diff"><span class="p">@@ -472,7 +472,7 @@</span><span class="idiff left right"> class ValidateData:</span></span>
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5129
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<pre style="margin: 0;">+<span id="LC5129" class="line" lang="diff"><span class="p">@@ -472,7 +472,7 @@</span></span>
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5122
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5130
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<pre style="margin: 0;"> <span id="LC5130" class="line" lang="diff"> </span>
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5123
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5131
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<pre style="margin: 0;"> <span id="LC5131" class="line" lang="diff"> #Check elements</span>
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5124
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5132
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<pre style="margin: 0;"> <span id="LC5132" class="line" lang="diff"> listSize = len(parameterValue)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5127,7 +5135,7 @@ index 5943240..d95222f 100755</td>
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5127
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5135
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<pre style="margin: 0;"> <span id="LC5135" class="line" lang="diff"> if(not ValidateData.funcIsValidString(parameterValue[i])):</span>
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5128
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<td class="diff-line-num new_line" data-linenumber="5136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5136
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<pre style="margin: 0;"> <span id="LC5136" class="line" lang="diff"> return False</span>
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5129
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5137
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<pre style="margin: 0;"> <span id="LC5137" class="line" lang="diff"> return True</span>
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<pre style="margin: 0;">-<span id="LC5130" class="line" lang="diff"><span class="p">@@ -520,7 +520,7 @@</span><span class="idiff left right"> class ValidateData:</span></span>
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5138
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<pre style="margin: 0;">+<span id="LC5138" class="line" lang="diff"><span class="p">@@ -520,7 +520,7 @@</span></span>
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5139
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<pre style="margin: 0;"> <span id="LC5139" class="line" lang="diff"> return False</span>
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5140
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<pre style="margin: 0;"> <span id="LC5140" class="line" lang="diff"> </span>
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5141
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<pre style="margin: 0;"> <span id="LC5141" class="line" lang="diff"> #Check key elements</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5136,7 +5144,7 @@ index 5943240..d95222f 100755</td>
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<pre style="margin: 0;"> <span id="LC5144" class="line" lang="diff"> keyListSize = len(keyList)</span>
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5145
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<pre style="margin: 0;"> <span id="LC5145" class="line" lang="diff"> for i in range(0,keyListSize):</span>
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5146
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<pre style="margin: 0;"> <span id="LC5146" class="line" lang="diff"> if keyList[i] == None:</span>
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<pre style="margin: 0;">-<span id="LC5139" class="line" lang="diff"><span class="p">@@ -530,7 +530,7 @@</span><span class="idiff left right"> class ValidateData:</span></span>
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<pre style="margin: 0;">+<span id="LC5147" class="line" lang="diff"><span class="p">@@ -530,7 +530,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC5148" class="line" lang="diff"> return False</span>
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5149
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<pre style="margin: 0;"> <span id="LC5149" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC5150" class="line" lang="diff"> #Check key elements</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5145,10 +5153,10 @@ index 5943240..d95222f 100755</td>
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<pre style="margin: 0;"> <span id="LC5153" class="line" lang="diff"> itemListSize = len(itemList)</span>
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<pre style="margin: 0;"> <span id="LC5154" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC5155" class="line" lang="diff"> for i in range(0,itemListSize):</span>
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<pre style="margin: 0;">-<span id="LC5148" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/plot_cladogram.py b</span>/plot_cladogram.py</span></span>
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<pre style="margin: 0;">-<span id="LC5149" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index 1b95358..0faba08 100755</span></span></span>
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<pre style="margin: 0;">-<span id="LC5150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/plot_cladogram.py</span></span></span>
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<pre style="margin: 0;">-<span id="LC5151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/plot_cladogram.py</span></span></span>
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<pre style="margin: 0;">+<span id="LC5156" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/plot_cladogram.py</span></span>
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<pre style="margin: 0;">+<span id="LC5157" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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<pre style="margin: 0;">+<span id="LC5158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/plot_cladogram.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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<pre style="margin: 0;">+<span id="LC5159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/plot_cladogram.py 2019-09-06 12:01:19.018688976 +0100</span></span></span>
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<pre style="margin: 0;"> <span id="LC5160" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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5161
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<pre style="margin: 0;"> <span id="LC5161" class="line" lang="diff"> import os,sys,matplotlib,argparse,string</span>
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<pre style="margin: 0;"> <span id="LC5162" class="line" lang="diff"> matplotlib.use('Agg')</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5158,7 +5166,7 @@ index 1b95358..0faba08 100755</td>
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5166
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<pre style="margin: 0;"> <span id="LC5166" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;"> <span id="LC5167" class="line" lang="diff"> </span>
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5168
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<pre style="margin: 0;"> <span id="LC5168" class="line" lang="diff"> colors = ['r','g','b','m','c',[1.0,0.5,0.0],[0.0,1.0,0.0],[0.33,0.125,0.0],[0.75,0.75,0.75],'k']</span>
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<pre style="margin: 0;">-<span id="LC5161" class="line" lang="diff"><span class="p">@@ -261,7 +261,7 @@</span><span class="idiff left right"> def plot_names(father,params,depth,ax,u_i,seps):</span></span>
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<pre style="margin: 0;">+<span id="LC5169" class="line" lang="diff"><span class="p">@@ -261,7 +261,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC5170" class="line" lang="diff"> lab = ""</span>
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5171
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<pre style="margin: 0;"> <span id="LC5171" class="line" lang="diff"> txt = father.last_name</span>
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<pre style="margin: 0;"> <span id="LC5172" class="line" lang="diff"> if params['abrv_start_lev'] < l <= params['abrv_stop_lev'] + 1:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5167,7 +5175,7 @@ index 1b95358..0faba08 100755</td>
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<pre style="margin: 0;"> <span id="LC5175" class="line" lang="diff"> lab = str(ide)+": "+father.last_name </span>
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5176
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<pre style="margin: 0;"> <span id="LC5176" class="line" lang="diff"> txt = str(ide)</span>
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5177
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<pre style="margin: 0;"> <span id="LC5177" class="line" lang="diff"> # ax.bar(fr_0, clto, width = fr_1-fr_0, bottom = float(l-1)/float(depth-1), alpha = params['alpha'], color=col, edgecolor=col)</span>
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<pre style="margin: 0;">-<span id="LC5170" class="line" lang="diff"><span class="p">@@ -288,7 +288,7 @@</span><span class="idiff left right"> def draw_tree(out_file,tree,params):</span></span>
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<pre style="margin: 0;">+<span id="LC5178" class="line" lang="diff"><span class="p">@@ -288,7 +288,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC5179" class="line" lang="diff"> params['clade_sep'] *= 0.75 </span>
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5180
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<pre style="margin: 0;"> <span id="LC5180" class="line" lang="diff"> seps = [params['clade_sep']*sep/(float(depth-i+1)*0.25) for i in range(1,len(tree['nlev'])+1)]</span>
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5181
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<pre style="margin: 0;"> <span id="LC5181" class="line" lang="diff"> totseps = sum([s*nlev[i] for i,s in enumerate(seps[:-1])])</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5176,10 +5184,10 @@ index 1b95358..0faba08 100755</td>
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5184
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<pre style="margin: 0;"> <span id="LC5184" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC5185" class="line" lang="diff"> fig = plt.figure(edgecolor=params['back_color'],facecolor=params['back_color'])</span>
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5186
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<pre style="margin: 0;"> <span id="LC5186" class="line" lang="diff"> ax = fig.add_subplot(111, polar=True, frame_on=False, axis_bgcolor=params['back_color'] )</span>
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<pre style="margin: 0;">-<span id="LC5179" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/plot_features.py b</span>/plot_features.py</span></span>
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5180
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<pre style="margin: 0;">-<span id="LC5180" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index 5371eb3..115cf61 100755</span></span></span>
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5181
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<pre style="margin: 0;">-<span id="LC5181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/plot_features.py</span></span></span>
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5182
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<pre style="margin: 0;">-<span id="LC5182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/plot_features.py</span></span></span>
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5187
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<pre style="margin: 0;">+<span id="LC5187" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/plot_features.py</span></span>
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5188
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<pre style="margin: 0;">+<span id="LC5188" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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5189
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<pre style="margin: 0;">+<span id="LC5189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/plot_features.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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5190
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<pre style="margin: 0;">+<span id="LC5190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/plot_features.py 2019-09-06 12:01:19.018688976 +0100</span></span></span>
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5183
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5191
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<pre style="margin: 0;"> <span id="LC5191" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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5184
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5192
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<pre style="margin: 0;"> <span id="LC5192" class="line" lang="diff"> import os,sys,matplotlib,zipfile,argparse,string</span>
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5193
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<pre style="margin: 0;"> <span id="LC5193" class="line" lang="diff"> matplotlib.use('Agg')</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5189,7 +5197,7 @@ index 5371eb3..115cf61 100755</td>
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5197
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<pre style="margin: 0;"> <span id="LC5197" class="line" lang="diff"> import random as rand</span>
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5190
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5198
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<pre style="margin: 0;"> <span id="LC5198" class="line" lang="diff"> </span>
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5199
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<pre style="margin: 0;"> <span id="LC5199" class="line" lang="diff"> colors = ['r','g','b','m','c']</span>
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5192
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<pre style="margin: 0;">-<span id="LC5192" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span><span class="idiff left right"> def read_data(file_data,file_feats,params):</span></span>
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5200
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<pre style="margin: 0;">+<span id="LC5200" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span></span>
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5201
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<pre style="margin: 0;"> <span id="LC5201" class="line" lang="diff"> with open(file_feats, 'r') as features:</span>
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5194
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5202
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<pre style="margin: 0;"> <span id="LC5202" class="line" lang="diff"> feats_to_plot = [(f.split()[:-1],len(f.split()) == 5) for f in features.readlines()]</span>
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5195
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5203
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<pre style="margin: 0;"> <span id="LC5203" class="line" lang="diff"> if not feats_to_plot:</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5198,7 +5206,7 @@ index 5371eb3..115cf61 100755</td>
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5198
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5206
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<pre style="margin: 0;"> <span id="LC5206" class="line" lang="diff"> sys.exit(0)</span>
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5199
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5207
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<pre style="margin: 0;"> <span id="LC5207" class="line" lang="diff"> feats,cls,class_sl,subclass_sl,class_hierarchy,params['norm_v'] = load_data(file_data, True) </span>
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5200
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5208
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<pre style="margin: 0;"> <span id="LC5208" class="line" lang="diff"> if params['feature_num'] > 0: </span>
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5201
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<td class="diff-line-num new_line old" data-linenumber="5209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5201" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span><span class="idiff left right"> def read_data(file_data,file_feats,params):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5209
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<pre style="margin: 0;">+<span id="LC5209" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span></span>
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5202
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<td class="diff-line-num new_line" data-linenumber="5210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5210
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<pre style="margin: 0;"> <span id="LC5210" class="line" lang="diff"> if params['f'] == "one" and f[0][0] != params['feature_name']: continue</span>
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<td class="diff-line-num old_line" data-linenumber="5203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5203
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<td class="diff-line-num new_line" data-linenumber="5211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5211
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<pre style="margin: 0;"> <span id="LC5211" class="line" lang="diff"> features[f[0][0]] = {'dim':float(f[0][1]), 'abundances':feats[f[0][0]], 'sig':f[1], 'cls':cls, 'class_sl':class_sl, 'subclass_sl':subclass_sl, 'class_hierarchy':class_hierarchy} </span>
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<td class="diff-line-num old_line" data-linenumber="5204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5204
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<td class="diff-line-num new_line" data-linenumber="5212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5212
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<pre style="margin: 0;"> <span id="LC5212" class="line" lang="diff"> if not features:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5207,7 +5215,7 @@ index 5371eb3..115cf61 100755</td>
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<td class="diff-line-num old_line" data-linenumber="5207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5207
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<td class="diff-line-num new_line" data-linenumber="5215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5215
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<pre style="margin: 0;"> <span id="LC5215" class="line" lang="diff"> sys.exit(0)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5208
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<td class="diff-line-num new_line" data-linenumber="5216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5216
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<pre style="margin: 0;"> <span id="LC5216" class="line" lang="diff"> return features</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5209
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<td class="diff-line-num new_line" data-linenumber="5217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5217
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<pre style="margin: 0;"> <span id="LC5217" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="5210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5210
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<td class="diff-line-num new_line old" data-linenumber="5218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5210" class="line" lang="diff"><span class="p">@@ -62,7 +62,7 @@</span><span class="idiff left right"> def plot(name,k_n,feat,params):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5218
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<pre style="margin: 0;">+<span id="LC5218" class="line" lang="diff"><span class="p">@@ -62,7 +62,7 @@</span></span>
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5211
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<td class="diff-line-num new_line" data-linenumber="5219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5219
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<pre style="margin: 0;"> <span id="LC5219" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="5212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5212
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<td class="diff-line-num new_line" data-linenumber="5220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5220
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<pre style="margin: 0;"> <span id="LC5220" class="line" lang="diff"> max_m = 0.0</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5213
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<td class="diff-line-num new_line" data-linenumber="5221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5221
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<pre style="margin: 0;"> <span id="LC5221" class="line" lang="diff"> norm = 1.0 if float(params['norm_v']) < 0.0 else float(params['norm_v'])</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5216,7 +5224,7 @@ index 5371eb3..115cf61 100755</td>
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<td class="diff-line-num old_line" data-linenumber="5216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5216
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5224
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<pre style="margin: 0;"> <span id="LC5224" class="line" lang="diff"> fr,to = v[0], v[1]</span>
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5217
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<td class="diff-line-num new_line" data-linenumber="5225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5225
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<pre style="margin: 0;"> <span id="LC5225" class="line" lang="diff"> median = numpy.mean(feat['abundances'][fr:to])</span>
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<td class="diff-line-num old_line" data-linenumber="5218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5218
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<td class="diff-line-num new_line" data-linenumber="5226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5226
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<pre style="margin: 0;"> <span id="LC5226" class="line" lang="diff"> if median > max_m: max_m = median</span>
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5219
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<td class="diff-line-num new_line old" data-linenumber="5227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5219" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</span><span class="idiff left right"> def plot(name,k_n,feat,params):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5227
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<pre style="margin: 0;">+<span id="LC5227" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</span></span>
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5220
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<td class="diff-line-num new_line" data-linenumber="5228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5228
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<pre style="margin: 0;"> <span id="LC5228" class="line" lang="diff"> if max_v == 0.0: max_v = 0.0001</span>
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<td class="diff-line-num old_line" data-linenumber="5221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5221
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<td class="diff-line-num new_line" data-linenumber="5229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5229
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<pre style="margin: 0;"> <span id="LC5229" class="line" lang="diff"> if max_v == min_v: max_v = min_v*1.1 </span>
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5222
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5230
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<pre style="margin: 0;"> <span id="LC5230" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5225,7 +5233,7 @@ index 5371eb3..115cf61 100755</td>
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5225
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5233
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<pre style="margin: 0;"> <span id="LC5233" class="line" lang="diff"> seps = []</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5226
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5234
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<pre style="margin: 0;"> <span id="LC5234" class="line" lang="diff"> xtics = []</span>
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5227
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5235
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<pre style="margin: 0;"> <span id="LC5235" class="line" lang="diff"> x2tics = []</span>
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5228
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<pre style="margin: 0;">-<span id="LC5228" class="line" lang="diff"><span class="p">@@ -142,8 +142,8 @@</span><span class="idiff left right"> if __name__ == '__main__':</span></span>
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5236
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<pre style="margin: 0;">+<span id="LC5236" class="line" lang="diff"><span class="p">@@ -142,8 +142,8 @@</span></span>
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5229
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5237
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<pre style="margin: 0;"> <span id="LC5237" class="line" lang="diff"> params['fore_color'] = 'w' if params['back_color'] == 'k' else 'k'</span>
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5230
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5238
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<pre style="margin: 0;"> <span id="LC5238" class="line" lang="diff"> features = read_data(params['input_file_1'],params['input_file_2'],params)</span>
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5231
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5239
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<pre style="margin: 0;"> <span id="LC5239" class="line" lang="diff"> if params['archive'] == "zip": file = zipfile.ZipFile(params['output_file'], "w")</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5236,11 +5244,11 @@ index 5371eb3..115cf61 100755</td>
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5236
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5244
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<pre style="margin: 0;"> <span id="LC5244" class="line" lang="diff"> if params['archive'] == "zip":</span>
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5237
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5245
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<pre style="margin: 0;"> <span id="LC5245" class="line" lang="diff"> of = plot("/tmp/"+str(int(f['sig']))+"_"+"-".join(k.split("."))+"."+params['format'],k,f,params)</span>
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5238
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5246
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<pre style="margin: 0;"> <span id="LC5246" class="line" lang="diff"> file.write(of, os.path.basename(of), zipfile.ZIP_DEFLATED)</span>
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5239
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<pre style="margin: 0;">-<span id="LC5239" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/plot_res.py b</span>/plot_res.py</span></span>
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5240
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<pre style="margin: 0;">-<span id="LC5240" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index f87e79e..e67153c 100755</span></span></span>
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5241
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<pre style="margin: 0;">-<span id="LC5241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/plot_res.py</span></span></span>
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<pre style="margin: 0;">-<span id="LC5242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/plot_res.py</span></span></span>
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5243
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<pre style="margin: 0;">-<span id="LC5243" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span><span class="idiff left right"> matplotlib.use('Agg')</span></span>
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<pre style="margin: 0;">+<span id="LC5247" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/plot_res.py</span></span>
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<pre style="margin: 0;">+<span id="LC5248" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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5249
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<pre style="margin: 0;">+<span id="LC5249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/plot_res.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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5250
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<pre style="margin: 0;">+<span id="LC5250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/plot_res.py 2019-09-06 12:01:19.022688949 +0100</span></span></span>
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<pre style="margin: 0;">+<span id="LC5251" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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5252
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<pre style="margin: 0;"> <span id="LC5252" class="line" lang="diff"> from pylab import *</span>
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5253
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<pre style="margin: 0;"> <span id="LC5253" class="line" lang="diff"> from collections import defaultdict</span>
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5254
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<pre style="margin: 0;"> <span id="LC5254" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5249,7 +5257,7 @@ index f87e79e..e67153c 100755</td>
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5257
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<pre style="margin: 0;"> <span id="LC5257" class="line" lang="diff"> import argparse</span>
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<td class="diff-line-num old_line" data-linenumber="5250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5250
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<td class="diff-line-num new_line" data-linenumber="5258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5258
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5258" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5251
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<td class="diff-line-num new_line" data-linenumber="5259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5259
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5259" class="line" lang="diff"> colors = ['r','g','b','m','c','y','k','w']</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5252
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<td class="diff-line-num new_line old" data-linenumber="5260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5252" class="line" lang="diff"><span class="p">@@ -44,7 +44,7 @@</span><span class="idiff left right"> def read_data(input_file,output_file,otu_only):</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5260
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<pre style="margin: 0;">+<span id="LC5260" class="line" lang="diff"><span class="p">@@ -44,7 +44,7 @@</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5253
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<td class="diff-line-num new_line" data-linenumber="5261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5261
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5261" class="line" lang="diff"> rows = [line.strip().split()[:-1] for line in inp.readlines() if len(line.strip().split())>3 and len(line.strip().split()[0].split('.'))==8] # a feature with length 8 will have an OTU id associated with it</span>
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<td class="diff-line-num old_line" data-linenumber="5254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5254
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<td class="diff-line-num new_line" data-linenumber="5262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5262
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5262" class="line" lang="diff"> classes = list(set([v[2] for v in rows if len(v)>2]))</span>
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<td class="diff-line-num old_line" data-linenumber="5255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5255
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<td class="diff-line-num new_line" data-linenumber="5263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5263
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5263" class="line" lang="diff"> if len(classes) < 1: </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5258,7 +5266,7 @@ index f87e79e..e67153c 100755</td>
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<td class="diff-line-num old_line" data-linenumber="5258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5258
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<td class="diff-line-num new_line" data-linenumber="5266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5266
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<pre style="margin: 0;"> <span id="LC5266" class="line" lang="diff"> os.system("touch "+output_file)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5259
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<td class="diff-line-num new_line" data-linenumber="5267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5267
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5267" class="line" lang="diff"> sys.exit()</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5260
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<td class="diff-line-num new_line" data-linenumber="5268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5268
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5268" class="line" lang="diff"> data = {}</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5261
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<td class="diff-line-num new_line old" data-linenumber="5269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5261" class="line" lang="diff"><span class="p">@@ -94,9 +94,9 @@</span><span class="idiff left right"> def plot_histo_hor(path,params,data,bcl,report_features):</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5269
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<pre style="margin: 0;">+<span id="LC5269" class="line" lang="diff"><span class="p">@@ -94,9 +94,9 @@</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5262
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<td class="diff-line-num new_line" data-linenumber="5270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5270
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5270" class="line" lang="diff"> ax.barh(pos[i],vv, align='center', color=col, label=lab, height=0.8, edgecolor=params['fore_color'])</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5263
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<td class="diff-line-num new_line" data-linenumber="5271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5271
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5271" class="line" lang="diff"> mv = max([abs(float(v[3])) for v in data['rows']]) </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5264
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<td class="diff-line-num new_line" data-linenumber="5272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5272
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5272" class="line" lang="diff"> if report_features:</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5270,7 +5278,7 @@ index f87e79e..e67153c 100755</td>
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<td class="diff-line-num old_line" data-linenumber="5270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5270
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<td class="diff-line-num new_line" data-linenumber="5278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5278
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5278" class="line" lang="diff"> for i,r in enumerate(data['rows']):</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5271
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<td class="diff-line-num new_line" data-linenumber="5279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5279
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5279" class="line" lang="diff"> indcl = cls.index(data['rows'][i][2])</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5272
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<td class="diff-line-num new_line" data-linenumber="5280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5280
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5280" class="line" lang="diff"> if params['n_scl'] < 0: rr = r[0]</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5273
</td>
<td class="diff-line-num new_line old" data-linenumber="5281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5273" class="line" lang="diff"><span class="p">@@ -156,9 +156,9 @@</span><span class="idiff left right"> def plot_histo_ver(path,params,data,report_features):</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5281
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<pre style="margin: 0;">+<span id="LC5281" class="line" lang="diff"><span class="p">@@ -156,9 +156,9 @@</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5274
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<td class="diff-line-num new_line" data-linenumber="5282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5282
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5282" class="line" lang="diff"> vv = fabs(float(v[3])) </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5275
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<td class="diff-line-num new_line" data-linenumber="5283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5283
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5283" class="line" lang="diff"> ax.bar(pos[i],vv, align='center', color=col, label=lab)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5276
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<td class="diff-line-num new_line" data-linenumber="5284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5284
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5284" class="line" lang="diff"> if report_features:</span>
</pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5282,11 +5290,11 @@ index f87e79e..e67153c 100755</td>
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5290
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<pre style="margin: 0;"> <span id="LC5290" class="line" lang="diff"> xticks(pos,nam,rotation=-20, ha = 'left',size=params['feature_font_size']) </span>
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5283
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5291
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<pre style="margin: 0;"> <span id="LC5291" class="line" lang="diff"> ax.set_title(params['title'],size=params['title_font_size'])</span>
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5284
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5292
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<pre style="margin: 0;"> <span id="LC5292" class="line" lang="diff"> ax.set_ylabel("LDA SCORE (log 10)")</span>
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5285
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<pre style="margin: 0;">-<span id="LC5285" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/qiime2lefse.py b</span>/qiime2lefse.py</span></span>
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5286
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<pre style="margin: 0;">-<span id="LC5286" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index dffecc3..cdd09ec 100755</span></span></span>
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5287
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<pre style="margin: 0;">-<span id="LC5287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/qiime2lefse.py</span></span></span>
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5288
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<pre style="margin: 0;">-<span id="LC5288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/qiime2lefse.py</span></span></span>
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5289
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<pre style="margin: 0;">-<span id="LC5289" class="line" lang="diff"><span class="p">@@ -43,8 +43,8 @@</span><span class="idiff left right"> def read_params(args):</span></span>
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<pre style="margin: 0;">+<span id="LC5293" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/qiime2lefse.py</span></span>
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<pre style="margin: 0;">+<span id="LC5294" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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5295
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<pre style="margin: 0;">+<span id="LC5295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/qiime2lefse.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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5296
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<pre style="margin: 0;">+<span id="LC5296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/qiime2lefse.py 2019-09-06 12:01:19.022688949 +0100</span></span></span>
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5297
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<pre style="margin: 0;">+<span id="LC5297" class="line" lang="diff"><span class="p">@@ -43,8 +43,8 @@</span></span>
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5290
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5298
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<pre style="margin: 0;"> <span id="LC5298" class="line" lang="diff"> def qiime2lefse( fin, fmd, fout, all_md, sel_md ):</span>
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5291
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5299
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<pre style="margin: 0;"> <span id="LC5299" class="line" lang="diff"> with (fin if fin==sys.stdin else open(fin)) as inpf :</span>
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5292
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5300
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<pre style="margin: 0;"> <span id="LC5300" class="line" lang="diff"> lines = [list(ll) for ll in </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5297,7 +5305,7 @@ index dffecc3..cdd09ec 100755</td>
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5305
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<pre style="margin: 0;"> <span id="LC5305" class="line" lang="diff"> for i,(l1,l2) in enumerate(zip( lines[0], lines[-1] )):</span>
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5298
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5306
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<pre style="margin: 0;"> <span id="LC5306" class="line" lang="diff"> if not l2 == 'Consensus Lineage':</span>
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5299
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5307
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<pre style="margin: 0;"> <span id="LC5307" class="line" lang="diff"> lines[-1][i] = l2+"|"+l1</span>
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5300
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<pre style="margin: 0;">-<span id="LC5300" class="line" lang="diff"><span class="p">@@ -59,17 +59,17 @@</span><span class="idiff left right"> def qiime2lefse( fin, fmd, fout, all_md, sel_md ):</span></span>
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5308
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<pre style="margin: 0;">+<span id="LC5308" class="line" lang="diff"><span class="p">@@ -59,17 +59,17 @@</span></span>
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5301
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5309
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<pre style="margin: 0;"> <span id="LC5309" class="line" lang="diff"> mdf = mdlines[0][1:]</span>
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5302
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5310
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<pre style="margin: 0;"> <span id="LC5310" class="line" lang="diff"> </span>
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5303
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5311
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<pre style="margin: 0;"> <span id="LC5311" class="line" lang="diff"> for l in mdlines:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5318,10 +5326,10 @@ index dffecc3..cdd09ec 100755</td>
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5318
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5326
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<pre style="margin: 0;"> <span id="LC5326" class="line" lang="diff"> if k == 'Consensus Lineage':</span>
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5319
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5327
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<pre style="margin: 0;"> <span id="LC5327" class="line" lang="diff"> continue</span>
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5320
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5328
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<pre style="margin: 0;"> <span id="LC5328" class="line" lang="diff"> out_m.append( [md[k][kmd] for kmd in selected_md] + list(v) )</span>
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5321
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<pre style="margin: 0;">-<span id="LC5321" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">diff --git a/run_lefse.py b</span>/run_lefse.py</span></span>
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5322
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<pre style="margin: 0;">-<span id="LC5322" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">index df248ef..98c42a3 100755</span></span></span>
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5323
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<pre style="margin: 0;">-<span id="LC5323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a/run_lefse.py</span></span></span>
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5324
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<pre style="margin: 0;">-<span id="LC5324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b/run_lefse.py</span></span></span>
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5329
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<pre style="margin: 0;">+<span id="LC5329" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">Index: lefse</span>/run_lefse.py</span></span>
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5330
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<pre style="margin: 0;">+<span id="LC5330" class="line" lang="diff"><span class="gh" style="color: #999;"><span class="idiff left right">===================================================================</span></span></span>
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5331
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<pre style="margin: 0;">+<span id="LC5331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lefse.orig/run_lefse.py 2019-09-06 12:01:19.030688896 +0100</span></span></span>
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5332
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<pre style="margin: 0;">+<span id="LC5332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lefse/run_lefse.py 2019-09-06 12:01:19.022688949 +0100</span></span></span>
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5325
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5333
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<pre style="margin: 0;"> <span id="LC5333" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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5326
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5334
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<pre style="margin: 0;"> <span id="LC5334" class="line" lang="diff"> #!/usr/bin/env python</span>
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5327
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5335
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<pre style="margin: 0;"> <span id="LC5335" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5331,7 +5339,7 @@ index df248ef..98c42a3 100755</td>
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5339
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<pre style="margin: 0;"> <span id="LC5339" class="line" lang="diff"> </span>
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5340
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<pre style="margin: 0;"> <span id="LC5340" class="line" lang="diff"> def read_params(args):</span>
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5341
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<pre style="margin: 0;"> <span id="LC5341" class="line" lang="diff"> parser = argparse.ArgumentParser(description='LEfSe 1.0')</span>
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<pre style="margin: 0;">-<span id="LC5334" class="line" lang="diff"><span class="p">@@ -60,38 +60,38 @@</span><span class="idiff left right"> if __name__ == '__main__':</span></span>
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<pre style="margin: 0;">+<span id="LC5342" class="line" lang="diff"><span class="p">@@ -60,38 +60,38 @@</span></span>
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<pre style="margin: 0;"> <span id="LC5343" class="line" lang="diff"> wilcoxon_res = {}</span>
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<pre style="margin: 0;"> <span id="LC5344" class="line" lang="diff"> kw_n_ok = 0</span>
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<pre style="margin: 0;"> <span id="LC5345" class="line" lang="diff"> nf = 0</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5381,7 +5389,7 @@ index df248ef..98c42a3 100755</td>
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5381
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5389
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<pre style="margin: 0;"> <span id="LC5389" class="line" lang="diff"> lda_res,lda_res_th = {},{}</span>
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5382
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5390
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<pre style="margin: 0;"> <span id="LC5390" class="line" lang="diff"> outres = {}</span>
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5383
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5391
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<pre style="margin: 0;"> <span id="LC5391" class="line" lang="diff"> outres['lda_res_th'] = lda_res_th</span>
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5384
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<pre style="margin: 0;">-<span id="LC5384" class="line" lang="diff"><span class="p">@@ -99,5 +99,5 @@</span><span class="idiff left right"> if __name__ == '__main__':</span></span>
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5392
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<pre style="margin: 0;">+<span id="LC5392" class="line" lang="diff"><span class="p">@@ -99,5 +99,5 @@</span></span>
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5385
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5393
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<pre style="margin: 0;"> <span id="LC5393" class="line" lang="diff"> outres['cls_means'] = cls_means</span>
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5386
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5394
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<pre style="margin: 0;"> <span id="LC5394" class="line" lang="diff"> outres['cls_means_kord'] = kord</span>
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5387
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<pre style="margin: 0;"> <span id="LC5395" class="line" lang="diff"> outres['wilcox_res'] = wilcoxon_res</span>
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