Mercurial > repos > iuc > vsnp_build_tables
changeset 2:a52b819aa990 draft
"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(-) [+] |
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--- 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']]