Mercurial > repos > peterjc > count_roi_variants
changeset 5:2ad9d74f97a8 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 7a746d55f0e8456992ee11c49a507285f9f39383-dirty
| author | peterjc |
|---|---|
| date | Fri, 03 Feb 2017 12:49:07 -0500 |
| parents | f7901a2a9d0c |
| children | fb728e40b5e0 |
| files | tools/count_roi_variants/count_roi_variants.py |
| diffstat | 1 files changed, 25 insertions(+), 6 deletions(-) [+] |
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--- a/tools/count_roi_variants/count_roi_variants.py Wed Feb 01 07:07:57 2017 -0500 +++ b/tools/count_roi_variants/count_roi_variants.py Fri Feb 03 12:49:07 2017 -0500 @@ -97,7 +97,9 @@ return answer -assert decode_cigar("14S15M1P1D3P54M1D34M5S") == [(14, 'S'), (15, 'M'), (1, 'P'), (1, 'D'), (3, 'P'), (54, 'M'), (1, 'D'), (34, 'M'), (5, 'S')] +assert decode_cigar("14S15M1P1D3P54M1D34M5S") == [(14, 'S'), (15, 'M'), (1, 'P'), + (1, 'D'), (3, 'P'), (54, 'M'), + (1, 'D'), (34, 'M'), (5, 'S')] def align_len(cigar_ops): @@ -144,10 +146,25 @@ 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("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): @@ -211,7 +228,9 @@ if return_code: sys.exit("Got return code %i from samtools view" % return_code) elif "specifies an unknown reference name. Continue anyway." in stderr: - sys.exit(stderr.strip() + "\n\nERROR: samtools did not recognise the region requested, can't count any variants.") + sys.exit(stderr.strip() + + "\n\nERROR: samtools did not recognise the region requested, " + "can't count any variants.") return tally