Mercurial > repos > devteam > complement
annotate gops_complement.py @ 4:1b2bfb9981b1 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
| author | devteam |
|---|---|
| date | Fri, 18 Dec 2015 19:37:08 -0500 |
| parents | 48d2f6a56a90 |
| children | 1377a23bc02a |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 """ | |
| 3 Complement regions. | |
| 4 | |
| 5 usage: %prog in_file out_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) | |
| 8 -a, --all: Complement all chromosomes (Genome-wide complement) | |
| 9 """ | |
| 10 | |
|
3
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
11 import sys |
|
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
12 import fileinput |
|
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
13 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper |
| 0 | 14 from bx.intervals.operations.complement import complement |
| 15 from bx.intervals.operations.subtract import subtract | |
| 16 from bx.cookbook import doc_optparse | |
|
3
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
17 from bx.tabular.io import ParseError |
|
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
18 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped |
| 0 | 19 |
| 20 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 21 | |
|
3
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
22 |
| 0 | 23 def main(): |
| 24 allchroms = False | |
| 25 | |
| 26 options, args = doc_optparse.parse( __doc__ ) | |
| 27 try: | |
| 28 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
| 29 lengths = options.lengths | |
|
3
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
30 if options.all: |
|
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
31 allchroms = True |
| 0 | 32 in_fname, out_fname = args |
| 33 except: | |
| 34 doc_optparse.exception() | |
| 35 | |
| 36 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), | |
| 37 chrom_col=chr_col_1, | |
| 38 start_col=start_col_1, | |
| 39 end_col=end_col_1, | |
| 40 strand_col=strand_col_1, | |
| 41 fix_strand=True ) | |
| 42 | |
| 43 lens = dict() | |
| 44 chroms = list() | |
| 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. | |
| 47 dbfile = fileinput.FileInput( lengths ) | |
|
3
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
48 |
| 0 | 49 if dbfile: |
| 50 if not allchroms: | |
| 51 try: | |
| 52 for line in dbfile: | |
| 53 fields = line.split("\t") | |
| 54 lens[fields[0]] = int(fields[1]) | |
| 55 except: | |
| 56 # assume LEN doesn't exist or is corrupt somehow | |
| 57 pass | |
| 58 elif allchroms: | |
| 59 try: | |
| 60 for line in dbfile: | |
| 61 fields = line.split("\t") | |
| 62 end = int(fields[1]) | |
|
3
48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
63 chroms.append("\t".join([fields[0], "0", str(end)])) |
| 0 | 64 except: |
| 65 pass | |
| 66 | |
| 67 # Safety...if the dbfile didn't exist and we're on allchroms, then | |
| 68 # default to generic complement | |
| 69 if allchroms and len(chroms) == 0: | |
| 70 allchroms = False | |
| 71 | |
| 72 if allchroms: | |
| 73 chromReader = GenomicIntervalReader(chroms) | |
| 74 generator = subtract([chromReader, g1]) | |
| 75 else: | |
| 76 generator = complement(g1, lens) | |
| 77 | |
| 78 out_file = open( out_fname, "w" ) | |
| 79 | |
| 80 try: | |
| 81 for interval in generator: | |
| 82 if type( interval ) is GenomicInterval: | |
| 83 out_file.write( "%s\n" % "\t".join( interval ) ) | |
| 84 else: | |
| 85 out_file.write( "%s\n" % interval ) | |
| 86 except ParseError, exc: | |
| 87 out_file.close() | |
| 88 fail( "Invalid file format: %s" % str( exc ) ) | |
| 89 | |
| 90 out_file.close() | |
| 91 | |
| 92 if g1.skipped > 0: | |
| 93 print skipped( g1, filedesc="" ) | |
| 94 | |
| 95 if __name__ == "__main__": | |
| 96 main() |