Mercurial > repos > devteam > basecoverage
annotate gops_basecoverage.py @ 5:37652c34b3bf draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author | devteam |
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date | Thu, 22 Jun 2017 18:37:49 -0400 |
parents | c929b6540d07 |
children | 4d584cf5ced5 |
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0 | 1 #!/usr/bin/env python |
2 """ | |
3 Count total base coverage. | |
4 | |
5 usage: %prog in_file out_file | |
6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file | |
7 """ | |
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37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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8 from __future__ import print_function |
0 | 9 |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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10 import fileinput |
c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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11 import sys |
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37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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12 |
37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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13 from bx.cookbook import doc_optparse |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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14 from bx.intervals.io import NiceReaderWrapper |
c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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15 from bx.intervals.operations.base_coverage import base_coverage |
c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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16 from bx.tabular.io import ParseError |
c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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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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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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21 |
0 | 22 def main(): |
23 options, args = doc_optparse.parse( __doc__ ) | |
24 try: | |
25 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
26 in_fname, out_fname = args | |
27 except: | |
28 doc_optparse.exception() | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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29 |
0 | 30 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), |
31 chrom_col=chr_col_1, | |
32 start_col=start_col_1, | |
33 end_col=end_col_1, | |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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34 strand_col=strand_col_1, |
0 | 35 fix_strand=True ) |
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c929b6540d07
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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36 |
0 | 37 try: |
38 bases = base_coverage(g1) | |
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37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
3
diff
changeset
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39 except ParseError as exc: |
0 | 40 fail( "Invalid file format: %s" % str( exc ) ) |
41 out_file = open( out_fname, "w" ) | |
42 out_file.write( "%s\n" % str( bases ) ) | |
43 out_file.close() | |
44 if g1.skipped > 0: | |
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37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
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diff
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45 print(skipped( g1, filedesc="" )) |
37652c34b3bf
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents:
3
diff
changeset
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46 |
0 | 47 |
48 if __name__ == "__main__": | |
49 main() |