Commit c41d2bae authored by Luis Pedro Coelho's avatar Luis Pedro Coelho

Line 85 in metaSNV.py:

Bugfix, add if clause to check header of bam file.

Line 31 of src/collapse_coverages.py:
Sort strings instead of integers to make the code more general. Now keys can be string or number, when sorting strings we get the same result.
parents e80e4429 ca7ed980
......@@ -82,9 +82,10 @@ def get_header(args):
line = line.rstrip().split('\t')
if len(line) != 3:
continue
line[1] = line[1].replace('SN:','')
line[2] = line[2].replace('LN:','')
f.write(line[1]+'\t1\t'+line[2]+'\n')
if line[0] == "@SQ":
line[1] = line[1].replace('SN:','')
line[2] = line[2].replace('LN:','')
f.write(line[1]+'\t1\t'+line[2]+'\n')
f.close()
args.ctg_len = args.project_dir + '/bed_header'
......@@ -270,4 +271,3 @@ SOLUTION: make\n\n'''.format(basedir))
if __name__ == '__main__':
main()
......@@ -28,7 +28,7 @@ def write_matrix(cov, header, ofile):
out.write('TaxId\t')
out.write('\t'.join([header for _ in bamfiles]))
out.write('\n')
for taxid in sorted(avg_cov.keys(), key=int):
for taxid in sorted(avg_cov.keys()):
c = cov[taxid]
out.write('{}\t'.format(taxid))
out.write('\t'.join([c[bf] for bf in bamfiles]))
......
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