comparison filter.py @ 5:49bf71fbc574 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed

4:aecfe10118ed

    for criterion in criteria:
        criterion.close()


def read_to_unmapped(read):
    '''
    Example unmapped read
    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

    Example mapped read:
    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----------------------------

    '''
    # TODO: rewrite read properties to unmapped state
    #       if colorspace: convert CS to NT directly
    #       remove excess tags

5:49bf71fbc574

    for criterion in criteria:
        criterion.close()


def read_to_unmapped(read):
    r'''
    Example unmapped read

    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

    Example mapped read:

    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----------------------------
    '''
    # TODO: rewrite read properties to unmapped state
    #       if colorspace: convert CS to NT directly
    #       remove excess tags