Mercurial > repos > peterjc > count_roi_variants
changeset 11:cc86a2b3dc8e draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 7138d537aaec46596985acf123348fe6f99cd6f1-dirty
| author | peterjc |
|---|---|
| date | Fri, 19 May 2017 06:19:10 -0400 |
| parents | 7a05cb080ea5 |
| children | 2429bebcab13 |
| files | tools/count_roi_variants/count_roi_variants.py |
| diffstat | 1 files changed, 37 insertions(+), 26 deletions(-) [+] |
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--- a/tools/count_roi_variants/count_roi_variants.py Thu May 11 12:43:27 2017 -0400 +++ b/tools/count_roi_variants/count_roi_variants.py Fri May 19 06:19:10 2017 -0400 @@ -37,7 +37,8 @@ AGCCCATGAGATGGGAAGCAATGGGCTACA 14 87.50 AGCCCATGAGATGGGAAGCAATGGGCTACG 1 6.25 AGCGCATGAGATGGGAAGCAATGGGCTACG 1 6.25 -""" +""" # noqa: E501 + if len(sys.argv) == 5: bam_filename, bai_filename, tabular_filename, region = sys.argv[1:] else: @@ -142,31 +143,41 @@ raise NotImplementedError("Unexpected CIGAR operator %s" % op) -assert list(expand_cigar("ACGT", decode_cigar("4M"))) == [(0, "A"), (1, "C"), (2, "G"), (3, "T")] -assert list(expand_cigar("ACGT", decode_cigar("2=1X1="))) == [(0, "A"), (1, "C"), (2, "G"), (3, "T")] -assert list(expand_cigar("ACGT", decode_cigar("2M1D2M"))) == [(0, "A"), (1, "C"), (3, "G"), (4, "T")] -assert list(expand_cigar("ACtGT", decode_cigar("2M1I2M"))) == [(0, "A"), (1, "C"), (1.5, "t"), (2, "G"), (3, "T")] -assert list(expand_cigar("tACGT", decode_cigar("1I4M"))) == [(-0.5, 't'), (0, 'A'), (1, 'C'), (2, 'G'), (3, 'T')] -assert list(expand_cigar("ACGTt", decode_cigar("4M1I"))) == [(0, 'A'), (1, 'C'), (2, 'G'), (3, 'T'), (3.5, 't')] -assert list(expand_cigar("AAAAGGGGTTTT", decode_cigar("12M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), - (3, 'A'), (4, 'G'), (5, 'G'), - (6, 'G'), (7, 'G'), (8, 'T'), - (9, 'T'), (10, 'T'), (11, 'T')] -assert list(expand_cigar("AAAAcGGGGTTTT", decode_cigar("4M1I8M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), - (3, 'A'), (3.5, 'c'), (4, 'G'), - (5, 'G'), (6, 'G'), (7, 'G'), - (8, 'T'), (9, 'T'), (10, 'T'), - (11, 'T')] -assert list(expand_cigar("AAAAGGGGcTTTT", decode_cigar("8M1I4M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), - (3, 'A'), (4, 'G'), (5, 'G'), - (6, 'G'), (7, 'G'), (7.5, "c"), - (8, 'T'), (9, 'T'), (10, 'T'), - (11, 'T')] -assert list(expand_cigar("AAAAcGGGGcTTTT", decode_cigar("4M1I4M1I4M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), - (3, 'A'), (3.5, 'c'), (4, 'G'), - (5, 'G'), (6, 'G'), (7, 'G'), - (7.5, 'c'), (8, 'T'), (9, 'T'), - (10, 'T'), (11, 'T')] +assert list(expand_cigar("ACGT", decode_cigar("4M"))) == \ + [(0, "A"), (1, "C"), (2, "G"), (3, "T")] +assert list(expand_cigar("ACGT", decode_cigar("2=1X1="))) == \ + [(0, "A"), (1, "C"), (2, "G"), (3, "T")] +assert list(expand_cigar("ACGT", decode_cigar("2M1D2M"))) == \ + [(0, "A"), (1, "C"), (3, "G"), (4, "T")] +assert list(expand_cigar("ACtGT", decode_cigar("2M1I2M"))) == \ + [(0, "A"), (1, "C"), (1.5, "t"), (2, "G"), (3, "T")] +assert list(expand_cigar("tACGT", decode_cigar("1I4M"))) == \ + [(-0.5, 't'), (0, 'A'), (1, 'C'), (2, 'G'), (3, 'T')] +assert list(expand_cigar("ACGTt", decode_cigar("4M1I"))) == \ + [(0, 'A'), (1, 'C'), (2, 'G'), (3, 'T'), (3.5, 't')] +assert list(expand_cigar("AAAAGGGGTTTT", decode_cigar("12M"))) == \ + [(0, 'A'), (1, 'A'), (2, 'A'), + (3, 'A'), (4, 'G'), (5, 'G'), + (6, 'G'), (7, 'G'), (8, 'T'), + (9, 'T'), (10, 'T'), (11, 'T')] +assert list(expand_cigar("AAAAcGGGGTTTT", decode_cigar("4M1I8M"))) == \ + [(0, 'A'), (1, 'A'), (2, 'A'), + (3, 'A'), (3.5, 'c'), (4, 'G'), + (5, 'G'), (6, 'G'), (7, 'G'), + (8, 'T'), (9, 'T'), (10, 'T'), + (11, 'T')] +assert list(expand_cigar("AAAAGGGGcTTTT", decode_cigar("8M1I4M"))) == \ + [(0, 'A'), (1, 'A'), (2, 'A'), + (3, 'A'), (4, 'G'), (5, 'G'), + (6, 'G'), (7, 'G'), (7.5, "c"), + (8, 'T'), (9, 'T'), (10, 'T'), + (11, 'T')] +assert list(expand_cigar("AAAAcGGGGcTTTT", decode_cigar("4M1I4M1I4M"))) == \ + [(0, 'A'), (1, 'A'), (2, 'A'), + (3, 'A'), (3.5, 'c'), (4, 'G'), + (5, 'G'), (6, 'G'), (7, 'G'), + (7.5, 'c'), (8, 'T'), (9, 'T'), + (10, 'T'), (11, 'T')] def get_roi(seq, cigar_ops, start, end):