[med-svn] [Git][med-team/mirtop][master] 4 commits: New upstream version 0.4.25

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / mirtop


Commits:
a3cd2ea9 by Nilesh Patra at 2022-05-29T11:23:18+05:30
New upstream version 0.4.25
- - - - -
96ba217d by Nilesh Patra at 2022-05-29T11:23:21+05:30
Update upstream source from tag 'upstream/0.4.25'

Update to upstream version '0.4.25'
with Debian dir ef38550465f3cf1d76cf99637c633405deac509c
- - - - -
2d2ab7d8 by Nilesh Patra at 2022-05-29T11:23:23+05:30
Bump Standards-Version to 4.6.1 (no changes needed)

- - - - -
a94be3ec by Nilesh Patra at 2022-05-29T11:23:36+05:30
Upload to unstable

- - - - -


5 changed files:

- HISTORY.md
- debian/changelog
- debian/control
- mirtop/gff/stats.py
- setup.py


Changes:

=====================================
HISTORY.md
=====================================
@@ -1,3 +1,7 @@
+0.4.25
+
+* [fix outliers samples](https://github.com/nf-core/smrnaseq/issues/137). When there is no identification of reference sequences or isomirs, the multiqc module will fails because it won't find the expected keys. Adding 0 when is the case.
+
 0.4.24
 
 * [fix bad](https://github.com/miRTop/mirtop/issues/64) annotation when 5 or more T/A at the end of the sequence by @DrHogart


=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+mirtop (0.4.25-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version 0.4.25
+  * Bump Standards-Version to 4.6.1 (no changes needed)
+
+ -- Nilesh Patra <nilesh at debian.org>  Sun, 29 May 2022 11:23:26 +0530
+
 mirtop (0.4.24-1) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-pybedtools,
                python3-pandas,
                python3-biopython
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/mirtop
 Vcs-Git: https://salsa.debian.org/med-team/mirtop.git
 Homepage: https://github.com/miRTop/mirtop


=====================================
mirtop/gff/stats.py
=====================================
@@ -103,6 +103,20 @@ def _classify(srna_type, attr, samples):
     return lines
 
 
+def _add_missing(df):
+    # ref_miRNA_mean
+    category = "ref_miRNA_mean"
+    if sum(df['category']==category) == 0:
+        df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0}
+        df = df.append(df2, ignore_index = True)
+    
+    category = "isomiR_sum"
+    if sum(df['category']==category) == 0:
+        df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0}
+        df = df.append(df2, ignore_index = True)
+    
+    return df
+
 def _summary(lines):
     """
     Summarize long table according to thresholds
@@ -113,10 +127,13 @@ def _summary(lines):
     df.counts = df.counts.astype(int)
     df_sum = df.groupby(['category', 'sample'], as_index=False).sum()
     df_sum['category'] = ["%s_sum" % r for r in df_sum['category']]
+    df_sum = _add_missing(df_sum)
     df_count = df.groupby(['category', 'sample'], as_index=False).count()
     df_count['category'] = ["%s_count" % r for r in df_count['category']]
+    df_count = _add_missing(df_count)
     df_mean = df.groupby(['category', 'sample'], as_index=False).mean()
     df_mean['category'] = ["%s_mean" % r for r in df_mean['category']]
+    df_mean = _add_missing(df_mean)
     df = pd.concat([df_sum, df_count, df_mean])
     return df
 


=====================================
setup.py
=====================================
@@ -3,7 +3,7 @@
 import os
 from setuptools import setup, find_packages
 
-version = '0.4.24'
+version = '0.4.25'
 
 url = 'http://github.com/mirtop/mirtop'
 



View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/12537e29c0c59516d61ab36261af49841b5a7a1b...a94be3ec19d66754437cd437bb99f0df7c280f3c

-- 
View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/12537e29c0c59516d61ab36261af49841b5a7a1b...a94be3ec19d66754437cd437bb99f0df7c280f3c
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