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annotate gops_complement.py @ 5:1377a23bc02a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
| author | devteam |
|---|---|
| date | Thu, 22 Jun 2017 18:38:23 -0400 |
| parents | 48d2f6a56a90 |
| children |
| 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 """ | |
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1377a23bc02a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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10 from __future__ import print_function |
| 0 | 11 |
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1377a23bc02a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
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changeset
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12 import fileinput |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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13 import sys |
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1377a23bc02a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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14 |
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1377a23bc02a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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changeset
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15 from bx.cookbook import doc_optparse |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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16 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper |
| 0 | 17 from bx.intervals.operations.complement import complement |
| 18 from bx.intervals.operations.subtract import subtract | |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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19 from bx.tabular.io import ParseError |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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20 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped |
| 0 | 21 |
| 22 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 23 | |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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24 |
| 0 | 25 def main(): |
| 26 allchroms = False | |
| 27 | |
| 28 options, args = doc_optparse.parse( __doc__ ) | |
| 29 try: | |
| 30 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
| 31 lengths = options.lengths | |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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32 if options.all: |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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33 allchroms = True |
| 0 | 34 in_fname, out_fname = args |
| 35 except: | |
| 36 doc_optparse.exception() | |
| 37 | |
| 38 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), | |
| 39 chrom_col=chr_col_1, | |
| 40 start_col=start_col_1, | |
| 41 end_col=end_col_1, | |
| 42 strand_col=strand_col_1, | |
| 43 fix_strand=True ) | |
| 44 | |
| 45 lens = dict() | |
| 46 chroms = list() | |
| 47 # dbfile is used to determine the length of each chromosome. The lengths | |
| 48 # are added to the lens dict and passed copmlement operation code in bx. | |
| 49 dbfile = fileinput.FileInput( lengths ) | |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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50 |
| 0 | 51 if dbfile: |
| 52 if not allchroms: | |
| 53 try: | |
| 54 for line in dbfile: | |
| 55 fields = line.split("\t") | |
| 56 lens[fields[0]] = int(fields[1]) | |
| 57 except: | |
| 58 # assume LEN doesn't exist or is corrupt somehow | |
| 59 pass | |
| 60 elif allchroms: | |
| 61 try: | |
| 62 for line in dbfile: | |
| 63 fields = line.split("\t") | |
| 64 end = int(fields[1]) | |
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48d2f6a56a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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65 chroms.append("\t".join([fields[0], "0", str(end)])) |
| 0 | 66 except: |
| 67 pass | |
| 68 | |
| 69 # Safety...if the dbfile didn't exist and we're on allchroms, then | |
| 70 # default to generic complement | |
| 71 if allchroms and len(chroms) == 0: | |
| 72 allchroms = False | |
| 73 | |
| 74 if allchroms: | |
| 75 chromReader = GenomicIntervalReader(chroms) | |
| 76 generator = subtract([chromReader, g1]) | |
| 77 else: | |
| 78 generator = complement(g1, lens) | |
| 79 | |
| 80 out_file = open( out_fname, "w" ) | |
| 81 | |
| 82 try: | |
| 83 for interval in generator: | |
| 84 if type( interval ) is GenomicInterval: | |
| 85 out_file.write( "%s\n" % "\t".join( interval ) ) | |
| 86 else: | |
| 87 out_file.write( "%s\n" % interval ) | |
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1377a23bc02a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
3
diff
changeset
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88 except ParseError as exc: |
| 0 | 89 out_file.close() |
| 90 fail( "Invalid file format: %s" % str( exc ) ) | |
| 91 | |
| 92 out_file.close() | |
| 93 | |
| 94 if g1.skipped > 0: | |
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5
1377a23bc02a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
3
diff
changeset
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95 print(skipped( g1, filedesc="" )) |
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1377a23bc02a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
3
diff
changeset
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96 |
| 0 | 97 |
| 98 if __name__ == "__main__": | |
| 99 main() |