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annotate gops_join.py @ 3:ffbd1de29c28 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:48:58 -0500 |
| parents | e56b47dce68a |
| children | a10f49d9218a |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 """ | |
| 3 Join two sets of intervals using their overlap as the key. | |
| 4 | |
| 5 usage: %prog bed_file_1 bed_file_2 out_file | |
| 6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file | |
| 7 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file | |
| 8 -m, --mincols=N: Require this much overlap (default 1bp) | |
| 9 -f, --fill=N: none, right, left, both | |
| 10 """ | |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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11 import fileinput |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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12 import sys |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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13 from bx.intervals.io import NiceReaderWrapper |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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14 from bx.intervals.operations.join import join |
| 0 | 15 from bx.cookbook import doc_optparse |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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16 from bx.tabular.io import ParseError |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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17 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped |
| 0 | 18 |
| 19 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 20 | |
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3
ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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21 |
| 0 | 22 def main(): |
| 23 mincols = 1 | |
| 24 leftfill = False | |
| 25 rightfill = False | |
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3
ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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26 |
| 0 | 27 options, args = doc_optparse.parse( __doc__ ) |
| 28 try: | |
| 29 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
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3
ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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30 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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diff
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31 if options.mincols: |
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ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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32 mincols = int( options.mincols ) |
| 0 | 33 if options.fill: |
| 34 if options.fill == "both": | |
| 35 rightfill = leftfill = True | |
| 36 else: | |
| 37 rightfill = options.fill == "right" | |
| 38 leftfill = options.fill == "left" | |
| 39 in_fname, in2_fname, out_fname = args | |
| 40 except: | |
| 41 doc_optparse.exception() | |
| 42 | |
| 43 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), | |
| 44 chrom_col=chr_col_1, | |
| 45 start_col=start_col_1, | |
| 46 end_col=end_col_1, | |
| 47 strand_col=strand_col_1, | |
| 48 fix_strand=True ) | |
| 49 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ), | |
| 50 chrom_col=chr_col_2, | |
| 51 start_col=start_col_2, | |
| 52 end_col=end_col_2, | |
| 53 strand_col=strand_col_2, | |
| 54 fix_strand=True ) | |
| 55 | |
| 56 out_file = open( out_fname, "w" ) | |
| 57 | |
| 58 try: | |
| 59 for outfields in join(g1, g2, mincols=mincols, rightfill=rightfill, leftfill=leftfill): | |
| 60 if type( outfields ) is list: | |
| 61 out_file.write( "%s\n" % "\t".join( outfields ) ) | |
| 62 else: | |
| 63 out_file.write( "%s\n" % outfields ) | |
| 64 except ParseError, exc: | |
| 65 out_file.close() | |
| 66 fail( "Invalid file format: %s" % str( exc ) ) | |
| 67 except MemoryError: | |
| 68 out_file.close() | |
| 69 fail( "Input datasets were too large to complete the join operation." ) | |
| 70 | |
| 71 out_file.close() | |
| 72 | |
| 73 if g1.skipped > 0: | |
| 74 print skipped( g1, filedesc=" of 1st dataset" ) | |
| 75 if g2.skipped > 0: | |
| 76 print skipped( g2, filedesc=" of 2nd dataset" ) | |
| 77 | |
| 78 if __name__ == "__main__": | |
| 79 main() |