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format the code and fix bug #7

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format the code and fix bug #7

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ce2f11f
1) replace index 2) formatter
Hocnonsense Aug 20, 2021
8668ddc
speed up for skip untracked seqs
Hocnonsense Aug 20, 2021
54d635e
1) fix bug: L252yminqual->minqual 2) formatter
Hocnonsense Aug 20, 2021
f3e9811
fix format
Hocnonsense Aug 20, 2021
8136088
speed up when initing
Hocnonsense Aug 21, 2021
bcbcae8
rename filterInputList to understandable name
Hocnonsense Aug 21, 2021
9f3330d
format " to '
Hocnonsense Aug 21, 2021
e330b66
BamFile.parse_gff genome support
Hocnonsense Aug 21, 2021
36eb80f
1) update doc of BamFile 2) fix Seq module bug
Hocnonsense Aug 21, 2021
d3a8010
fix: right indent of updating base_stats
Hocnonsense Aug 21, 2021
df4f61c
update BamContig.annotation
Hocnonsense Aug 21, 2021
d76f4bd
update BamConfig.get_base_stats_for_poly, stage 1
Hocnonsense Aug 21, 2021
7e38dda
fix: duplite name
Hocnonsense Aug 21, 2021
fdf58fa
update version and TODO
Hocnonsense Aug 21, 2021
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6 changes: 3 additions & 3 deletions cmseq/breadth_depth.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def bd_from_file():
si = True if args.sortindex else False
mode = 'all' if args.f else 'nofilter'

bf = BamFile(args.BAMFILE,sort=si,index=si,stepper=mode,minlen=args.minlen,filterInputList=args.contig,minimumReadsAligning=args.mincov)
bf = BamFile(args.BAMFILE,sort=si,index=si,stepper=mode,minlen=args.minlen,filtRefGenomes=args.contig,minimumReadsAligning=args.mincov)

print('Contig\tBreadth\tDepth avg\tDepth median')

Expand All @@ -37,7 +37,7 @@ def bd_from_file():

if not all(np.isnan(x) for x in [bd_result[0],bd_result[1],bd_result[2]]):
print (i.name+'\t'+str(bd_result[0])+'\t'+str(bd_result[1])+'\t'+str(bd_result[2]))

if args.combine:
all_coverage_values.extend(bd_result[3])

Expand All @@ -49,4 +49,4 @@ def bd_from_file():


if __name__ == "__main__":
bd_from_file()
bd_from_file()
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