root/galaxy-central/eggs/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.6.egg/genetrack/scripts/eland2gff.py

リビジョン 3, 2.9 KB (コミッタ: kohda, 14 年 前)

Install Unix tools  http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html

行番号 
1"""
2Eland file transformer. Transforms an eland file
3to a gff file format.
4
5    python eland2gff.py
6
7As a python module::
8
9    python -m genetrack.scripts.eland2gff
10
11Or in other python scripts::
12
13>>>
14>>> from genetrack.scripts import eland2gff
15>>> eland2gff.transform(inpname, outname)
16>>>
17
18Run the script with no parameters to see the options that it takes.
19
20**Observed runtime**: tranformation rate of 5 million lines per minute
21
22"""
23import os, sys, csv
24from itertools import *
25from genetrack import logger, conf, util
26
27
28def transform(inpname, size, outname=None):
29    """
30    Transforms reads stored in bedfile to a genetrack input file.
31    Requires at least 6 bed columns to access the strand.
32    """
33    logger.debug('input %s' % inpname)
34    logger.debug('output %s' % outname)
35
36    reader = csv.reader(open(inpname), delimiter='\t')
37
38    # unwind the iterator
39    list(takewhile( lambda x: x[0].startswith('#'), reader))
40
41    output = file(outname, 'wt')
42    output.write('##gff-version 3\n')
43    output.write('# created with eland2gff on %s\n' % inpname)
44    output.write('# fixed read lenght of %s\n' % size)
45    for row in reader:
46        chrom, start, strand = row[10], int(row[12]), row[13]
47        end = start + size
48        if strand == 'F':
49            strand = '+'
50        else:
51            strand = '-'
52        result = map(str, [chrom, '.', '.', start, end, '.', strand, '.', '.'])
53        output.write("%s\n" % '\t'.join(result))
54   
55    output.close()
56
57def option_parser():
58    "The option parser may be constructed in other tools invoking this script"
59    import optparse
60
61    usage = "usage: %prog -i inputfile -o outputfile"
62
63    parser = optparse.OptionParser(usage=usage)
64
65    # setting the input file name
66    parser.add_option(
67        '-i', '--input', action="store",
68        dest="inpname", type='str', default=None,
69        help="the input file name (required)"
70    )
71
72    # setting the output file name
73    parser.add_option(
74        '-o', '--output', action="store",
75        dest="outname", type='str', default=None,
76        help="output file name (optional)"
77    )
78
79    # verbosity can be 0,1 and 2 (increasing verbosity)
80    parser.add_option(
81        '-v', '--verbosity', action="store",
82        dest="verbosity", type="int", default=1,
83        help="sets the verbosity (0, 1) (default=1)",
84    )
85
86    # correction shift added in 5' direction for start/end coordinates
87    parser.add_option(
88        '-s', '--size', action="store",
89        dest="size", type="int", default=36,
90        help="readlength (fixed) default 36",
91    )
92
93    return parser
94
95if __name__ == '__main__':
96   
97    parser = option_parser()
98
99    options, args = parser.parse_args()
100
101    # set verbosity
102    logger.disable(options.verbosity)
103
104    # missing file names
105    if not options.inpname:
106        parser.print_help()
107    else:
108        options.outname=options.outname or '%s.gff' % options.inpname
109        transform(inpname=options.inpname, outname=options.outname, size=options.size)
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