Mercurial > repos > iuc > variant_analyzer
diff mut2sscs.py @ 1:3556001ff2db draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
| author | iuc |
|---|---|
| date | Wed, 04 Dec 2019 16:21:17 -0500 |
| parents | 8d29173d49a9 |
| children | 3f1dbd2c59bf |
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--- a/mut2sscs.py Wed Nov 20 17:47:35 2019 -0500 +++ b/mut2sscs.py Wed Dec 04 16:21:17 2019 -0500 @@ -56,7 +56,7 @@ # 1. read mut file with open(file1, 'r') as mut: - mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype='string') + mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str) # 2 read SSCS bam file # pysam.index(file2) @@ -76,7 +76,7 @@ ref = mut_array[m, 9] alt = mut_array[m, 10] - for pileupcolumn in bam.pileup(chrom.tobytes(), stop_pos - 2, stop_pos, max_depth=1000000000): + for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=1000000000): if pileupcolumn.reference_pos == stop_pos - 1: count_alt = 0 count_ref = 0