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annotate gops_coverage.py @ 4:ad25eb2c422d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
| author | devteam |
|---|---|
| date | Thu, 22 Jun 2017 18:39:05 -0400 |
| parents | 7b226a8a6722 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 """ | |
| 3 Calculate coverage of one query on another, and append the coverage to | |
| 4 the last two columns as bases covered and percent coverage. | |
| 5 | |
| 6 usage: %prog bed_file_1 bed_file_2 out_file | |
| 7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file | |
| 8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file | |
| 9 """ | |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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10 from __future__ import print_function |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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11 |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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12 import fileinput |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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13 import sys |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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14 |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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changeset
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15 from bx.cookbook import doc_optparse |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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16 from bx.intervals.io import GenomicInterval, NiceReaderWrapper |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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17 from bx.intervals.operations.coverage import coverage |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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18 from bx.tabular.io import ParseError |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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19 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped |
| 0 | 20 |
| 21 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 22 | |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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23 |
| 0 | 24 def main(): |
| 25 options, args = doc_optparse.parse( __doc__ ) | |
| 26 try: | |
| 27 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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28 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) |
| 0 | 29 in_fname, in2_fname, out_fname = args |
| 30 except: | |
| 31 doc_optparse.exception() | |
| 32 | |
| 33 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), | |
| 34 chrom_col=chr_col_1, | |
| 35 start_col=start_col_1, | |
| 36 end_col=end_col_1, | |
| 37 strand_col=strand_col_1, | |
| 38 fix_strand=True ) | |
| 39 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ), | |
| 40 chrom_col=chr_col_2, | |
| 41 start_col=start_col_2, | |
| 42 end_col=end_col_2, | |
| 43 strand_col=strand_col_2, | |
| 44 fix_strand=True ) | |
| 45 | |
| 46 out_file = open( out_fname, "w" ) | |
| 47 | |
| 48 try: | |
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7b226a8a6722
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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49 for line in coverage( [g1, g2] ): |
| 0 | 50 if type( line ) is GenomicInterval: |
| 51 out_file.write( "%s\n" % "\t".join( line.fields ) ) | |
| 52 else: | |
| 53 out_file.write( "%s\n" % line ) | |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
2
diff
changeset
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54 except ParseError as exc: |
| 0 | 55 out_file.close() |
| 56 fail( "Invalid file format: %s" % str( exc ) ) | |
| 57 | |
| 58 out_file.close() | |
| 59 | |
| 60 if g1.skipped > 0: | |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
2
diff
changeset
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61 print(skipped( g1, filedesc=" of 1st dataset" )) |
| 0 | 62 if g2.skipped > 0: |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
2
diff
changeset
|
63 print(skipped( g2, filedesc=" of 2nd dataset" )) |
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ad25eb2c422d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
2
diff
changeset
|
64 |
| 0 | 65 |
| 66 if __name__ == "__main__": | |
| 67 main() |