Mercurial > repos > iuc > ngsutils_bam_filter

comparison filter.py @ 8:bc31eb2abd1a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 19:13:53 -0400
parents 65c2eb88b635
children 3bda2c2b1cf8
comparison
equal deleted inserted replaced
7:c1b7608bb4b3 8:bc31eb2abd1a
913 for criterion in criteria: 913 for criterion in criteria:
914 criterion.close() 914 criterion.close()
915 915
916 916
917 def read_to_unmapped(read): 917 def read_to_unmapped(read):
918 ''' 918 r'''
919 Example unmapped read 919 Example unmapped read
920
920 2358_2045_1839 | 4 | * | 0 | 0 | * | * | 0 | 0 | GGACGAGAAGGAGTATTTCTCCGAGAACACATTCACGGAGAGTCTAACTC | 0QT\VNO^IIRJKXTIHIKTY\STZZ[XOJKPWLHJQQQ^XPQYIIRQII | PG:Z:bfast | AS:i:- | NH:i:0 | IH:i:1 | HI:i:1 | CS:Z:T10213222020221330022203222011113021130222212230122 | CQ:Z:019=2+><%@.'>52%)'15?90<7;:5+(-49('-7-<>5-@5%<.2%= | CM:i:0 | XA:i:4 921 2358_2045_1839 | 4 | * | 0 | 0 | * | * | 0 | 0 | GGACGAGAAGGAGTATTTCTCCGAGAACACATTCACGGAGAGTCTAACTC | 0QT\VNO^IIRJKXTIHIKTY\STZZ[XOJKPWLHJQQQ^XPQYIIRQII | PG:Z:bfast | AS:i:- | NH:i:0 | IH:i:1 | HI:i:1 | CS:Z:T10213222020221330022203222011113021130222212230122 | CQ:Z:019=2+><%@.'>52%)'15?90<7;:5+(-49('-7-<>5-@5%<.2%= | CM:i:0 | XA:i:4
921 922
922 Example mapped read: 923 Example mapped read:
924
923 2216_1487_198 | 16 | chr11:19915291-19925392 | 5531 | 12 | 24M2D26M | * | 0 | 0 | TCTGTCTGGGTGCAGTAGCTATACGTAATCCCAGCACTTTGGGAGGCCAA | 1C8FZ`M""""""WZ""%"#\I;"`R@D]``ZZ``\QKX\Y]````IK^` | PG:Z:bfast | AS:i:1150 | NM:i:2 | NH:i:10 | IH:i:1 | HI:i:1 | MD:Z:24^CT26 | CS:Z:T00103022001002113210023031213331122121223321221122 | CQ:Z:A8=%;AB<;97<3/9:>>3>@?5&18@-%;866:94=14:=?,%?:7&)1 | CM:i:9 | XA:i:4 | XE:Z:-------23322---2-11----2---------------------------- 925 2216_1487_198 | 16 | chr11:19915291-19925392 | 5531 | 12 | 24M2D26M | * | 0 | 0 | TCTGTCTGGGTGCAGTAGCTATACGTAATCCCAGCACTTTGGGAGGCCAA | 1C8FZ`M""""""WZ""%"#\I;"`R@D]``ZZ``\QKX\Y]````IK^` | PG:Z:bfast | AS:i:1150 | NM:i:2 | NH:i:10 | IH:i:1 | HI:i:1 | MD:Z:24^CT26 | CS:Z:T00103022001002113210023031213331122121223321221122 | CQ:Z:A8=%;AB<;97<3/9:>>3>@?5&18@-%;866:94=14:=?,%?:7&)1 | CM:i:9 | XA:i:4 | XE:Z:-------23322---2-11----2----------------------------
924
925 ''' 926 '''
926 # TODO: rewrite read properties to unmapped state 927 # TODO: rewrite read properties to unmapped state
927 # if colorspace: convert CS to NT directly 928 # if colorspace: convert CS to NT directly
928 # remove excess tags 929 # remove excess tags
929 930