Mercurial > repos > devteam > complement
comparison gops_complement.py @ 3:e0a23ab32d7f draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:47:38 -0500 |
parents | d958d5a0d1e8 |
children | 38c8bb402872 |
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2:2221cf5f59aa | 3:e0a23ab32d7f |
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6 -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file | 6 -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file |
7 -l, --lengths=N: Filename of .len file for species (chromosome lengths) | 7 -l, --lengths=N: Filename of .len file for species (chromosome lengths) |
8 -a, --all: Complement all chromosomes (Genome-wide complement) | 8 -a, --all: Complement all chromosomes (Genome-wide complement) |
9 """ | 9 """ |
10 | 10 |
11 import sys, traceback, fileinput | 11 import sys |
12 from warnings import warn | 12 import fileinput |
13 from bx.intervals import * | 13 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper |
14 from bx.intervals.io import * | |
15 from bx.intervals.operations.complement import complement | 14 from bx.intervals.operations.complement import complement |
16 from bx.intervals.operations.subtract import subtract | 15 from bx.intervals.operations.subtract import subtract |
17 from bx.cookbook import doc_optparse | 16 from bx.cookbook import doc_optparse |
18 from galaxy.tools.util.galaxyops import * | 17 from bx.tabular.io import ParseError |
18 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped | |
19 | 19 |
20 assert sys.version_info[:2] >= ( 2, 4 ) | 20 assert sys.version_info[:2] >= ( 2, 4 ) |
21 | 21 |
22 | |
22 def main(): | 23 def main(): |
23 allchroms = False | 24 allchroms = False |
24 upstream_pad = 0 | |
25 downstream_pad = 0 | |
26 | 25 |
27 options, args = doc_optparse.parse( __doc__ ) | 26 options, args = doc_optparse.parse( __doc__ ) |
28 try: | 27 try: |
29 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | 28 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) |
30 lengths = options.lengths | 29 lengths = options.lengths |
31 if options.all: allchroms = True | 30 if options.all: |
31 allchroms = True | |
32 in_fname, out_fname = args | 32 in_fname, out_fname = args |
33 except: | 33 except: |
34 doc_optparse.exception() | 34 doc_optparse.exception() |
35 | 35 |
36 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), | 36 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), |
43 lens = dict() | 43 lens = dict() |
44 chroms = list() | 44 chroms = list() |
45 # dbfile is used to determine the length of each chromosome. The lengths | 45 # dbfile is used to determine the length of each chromosome. The lengths |
46 # are added to the lens dict and passed copmlement operation code in bx. | 46 # are added to the lens dict and passed copmlement operation code in bx. |
47 dbfile = fileinput.FileInput( lengths ) | 47 dbfile = fileinput.FileInput( lengths ) |
48 | 48 |
49 if dbfile: | 49 if dbfile: |
50 if not allchroms: | 50 if not allchroms: |
51 try: | 51 try: |
52 for line in dbfile: | 52 for line in dbfile: |
53 fields = line.split("\t") | 53 fields = line.split("\t") |
58 elif allchroms: | 58 elif allchroms: |
59 try: | 59 try: |
60 for line in dbfile: | 60 for line in dbfile: |
61 fields = line.split("\t") | 61 fields = line.split("\t") |
62 end = int(fields[1]) | 62 end = int(fields[1]) |
63 chroms.append("\t".join([fields[0],"0",str(end)])) | 63 chroms.append("\t".join([fields[0], "0", str(end)])) |
64 except: | 64 except: |
65 pass | 65 pass |
66 | 66 |
67 # Safety...if the dbfile didn't exist and we're on allchroms, then | 67 # Safety...if the dbfile didn't exist and we're on allchroms, then |
68 # default to generic complement | 68 # default to generic complement |