Mercurial > repos > iuc > vsnp_build_tables

changeset 2:a52b819aa990 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 94e69abb568077267eb8b15ef624624e2899a750"
author iuc
date Wed, 30 Sep 2020 19:07:23 +0000
parents 0bc0009f9ea0
children 85587c8eb25f
files vsnp_add_zero_coverage.py vsnp_build_tables.py
diffstat 2 files changed, 7 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/vsnp_add_zero_coverage.py	Sun Sep 27 10:08:14 2020 +0000
+++ b/vsnp_add_zero_coverage.py	Wed Sep 30 19:07:23 2020 +0000
@@ -3,11 +3,12 @@
 import argparse
 import multiprocessing
 import os
-import pandas
-import pysam
 import queue
 import re
 import shutil
+
+import pandas
+import pysam
 from Bio import SeqIO
 
 INPUT_BAM_DIR = 'input_bam_dir'
--- a/vsnp_build_tables.py	Sun Sep 27 10:08:14 2020 +0000
+++ b/vsnp_build_tables.py	Wed Sep 30 19:07:23 2020 +0000
@@ -3,10 +3,11 @@
 import argparse
 import multiprocessing
 import os
+import queue
+import re
+
 import pandas
-import queue
 import pandas.io.formats.excel
-import re
 from Bio import SeqIO
 
 INPUT_JSON_AVG_MQ_DIR = 'input_json_avg_mq_dir'
@@ -32,7 +33,7 @@
         # Create an annotation file.
         annotation_file = "%s_annotations.csv" % group
         with open(annotation_file, "a") as fh:
-            for index, row in positions.iterrows():
+            for _, row in positions.iterrows():
                 pos = row.position
                 try:
                     aaa = pro.iloc[pro.index.get_loc(int(pos))][['chrom', 'locus', 'product', 'gene']]