[med-svn] [pipasic] 03/03: More fixes needed to pass the test suite

[Andreas Tille]

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tille pushed a commit to branch master
in repository pipasic.

commit 87553d666fa3d02b948d7503a648ed2d301dadea
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 2 15:21:21 2015 +0200

    More fixes needed to pass the test suite
---
 debian/patches/check_output_option_for_file.patch | 18 +++++++++++++
 debian/patches/ensure_output_dir.patch            | 21 +++++++++++++++
 debian/patches/safe_path_names.patch              | 33 +++++++++++++++++++++++
 debian/patches/series                             |  3 +++
 4 files changed, 75 insertions(+)

diff --git a/debian/patches/check_output_option_for_file.patch b/debian/patches/check_output_option_for_file.patch
new file mode 100644
index 0000000..7a378ac
--- /dev/null
+++ b/debian/patches/check_output_option_for_file.patch
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at debian.org>
+Last-update: Tue, 29 Sep 2015 15:21:50 +0200
+Description: The doc for the eyample dataset mentions "-o test_results/" which is
+ plain wrong according to the code a file needs to be specified.  Enabling
+ accepting a directory as well.
+
+--- a/pipasic.py
++++ b/pipasic.py
+@@ -85,6 +85,9 @@ Note: Pipasic requires two .fasta for ea
+ 	if not outfile:
+ 		print "No output filename given. Writing all output to working directory, 'output'-files\n"
+ 		outfile = "output.txt"
++	if outfile.endswith('/'):
++		print "given output target is a directory - appending 'output.txt' ...\n"
++		outfile = os.path.join(outfile, 'output.txt')
+ 	labels = options.labels
+ 	if labels:
+ 		labels = labels.split(",")
diff --git a/debian/patches/ensure_output_dir.patch b/debian/patches/ensure_output_dir.patch
new file mode 100644
index 0000000..cc95282
--- /dev/null
+++ b/debian/patches/ensure_output_dir.patch
@@ -0,0 +1,21 @@
+Author: Andreas Tille <tille at debian.org>
+Last-update: Tue, 29 Sep 2015 15:21:50 +0200
+Description: Ensure the output directory exists
+
+--- a/pipasic.py
++++ b/pipasic.py
+@@ -132,7 +132,13 @@ Note: Pipasic requires two .fasta for ea
+ 							print "Could not find PSM-file '%s' for %s and %s" %(inspectOut,spec,DB)
+ 							sample_counts.append(0)
+ 					countList.append(sample_counts)
+-			np.array(countList).dump(os.path.splitext(outfile)[0]+"_counts.dat")
++			outputdir=os.path.splitext(outfile)[0]
++			try: 
++				os.makedirs(outputdir)
++			except OSError:
++				if not os.path.isdir(outputdir):
++					raise
++			np.array(countList).dump(os.path.join(outputdir,"_counts.dat"))
+ 		else:
+ 			print "Aborting. - Spectra and reference proteomes needed as the arguments!"
+ 			optparser.print_help()
diff --git a/debian/patches/safe_path_names.patch b/debian/patches/safe_path_names.patch
index 72aab99..be99b7f 100644
--- a/debian/patches/safe_path_names.patch
+++ b/debian/patches/safe_path_names.patch
@@ -75,6 +75,24 @@ Description: Make sure directory and file are properly separated
  						try: 
  							count = parseInspect(inpath=inspectOut,fdr_countcut=fdr,silent=False)[1]
  							sample_counts.append(count)
+@@ -150,7 +150,7 @@ Note: Pipasic requires two .fasta for ea
+ 			print "Aborting. - Reference proteomes needed as (only or 2nd) argument!"
+ 			optparser.print_help()
+ 			sys.exit(1)
+-		dbList = ",".join([options.db_dir+db+".fasta" for db in db_list])
++		dbList = ",".join([os.path.join(options.db_dir,db+".fasta") for db in db_list])
+ 		from trypticpeptides import unweightedMatrix
+ 		simiMat_unw = unweightedMatrix(dbList=dbList, verbose=verbose)
+ 		np.array(simiMat_unw).dump(os.path.splitext(outfile)[0]+"_M_unw.dat")
+@@ -160,7 +160,7 @@ Note: Pipasic requires two .fasta for ea
+ 		if len(args) == 2:
+ 			spectra = args[0].split(',')
+ 			db_list = args[1].split(',')
+-			dbList = ",".join([options.db_dir+db+".fasta" for db in db_list])
++			dbList = ",".join([os.path.join(options.db_dir,db+".fasta") for db in db_list])
+ 		else:
+ 			print "Aborting. - Spectra and reference proteomes needed as the arguments!"
+ 			optparser.print_help()
 @@ -168,7 +168,7 @@ Note: Pipasic requires two .fasta for ea
  		from trypticpeptides import weightedMatrix
  		M_list_wtd = []
@@ -93,3 +111,18 @@ Description: Make sure directory and file are properly separated
  					try: 
  						count = parseInspect(inpath=inspectOut,fdr_countcut=fdr,silent=False)[1]
  						sample_counts.append(count)
+--- a/plotting.py
++++ b/plotting.py
+@@ -58,9 +58,9 @@ plot PASiC results.
+ 	if len(args) < 2:
+ 		command_parser.print_help()
+ 		sys.exit(1)
+-	obs  = np.load(options.f_dir+args[0])
+-	corr = np.load(options.f_dir+args[1])
+-	if len(args) > 2: wtd = np.load(options.f_dir+args[2])
++	obs  = np.load(os.path.join(options.f_dir,args[0]))
++	corr = np.load(os.path.join(options.f_dir,args[1]))
++	if len(args) > 2: wtd = np.load(os.path.join(options.f_dir,args[2]))
+ 	else: wtd = []
+ 	input_tags = options.tags.split(",")
+ 	if options.names: names = options.names.split(",")
diff --git a/debian/patches/series b/debian/patches/series
index 2bb5a96..fc34d87 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,6 @@ inspect_files.patch
 verbosity.patch
 safe_path_names.patch
 config.patch
+ensure_output_dir.patch
+# debug.patch
+check_output_option_for_file.patch

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