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annotate gops_coverage.py @ 4:e3363e087468 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9
author devteam
date Mon, 13 Jun 2022 16:21:57 +0000
parents 4ef9819dc7fb
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1 #!/usr/bin/env python
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2 """
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3 Calculate coverage of one query on another, and append the coverage to
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4 the last two columns as bases covered and percent coverage.
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5
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6 usage: %prog bed_file_1 bed_file_2 out_file
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7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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9 """
3
4ef9819dc7fb 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
4ef9819dc7fb 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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12 import fileinput
bc9c66c1e9c9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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13 import sys
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14
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15 from bx.cookbook import doc_optparse
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16 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
bc9c66c1e9c9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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17 from bx.intervals.operations.coverage import coverage
bc9c66c1e9c9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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18 from bx.tabular.io import ParseError
bc9c66c1e9c9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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19 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
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20
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21 assert sys.version_info[:2] >= ( 2, 4 )
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22
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23
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24 def main():
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25 options, args = doc_optparse.parse( __doc__ )
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26 try:
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27 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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28 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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29 in_fname, in2_fname, out_fname = args
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30 except:
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31 doc_optparse.exception()
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32
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33 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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34 chrom_col=chr_col_1,
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35 start_col=start_col_1,
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36 end_col=end_col_1,
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37 strand_col=strand_col_1,
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38 fix_strand=True )
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39 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
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40 chrom_col=chr_col_2,
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41 start_col=start_col_2,
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42 end_col=end_col_2,
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43 strand_col=strand_col_2,
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44 fix_strand=True )
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45
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46 out_file = open( out_fname, "w" )
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47
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48 try:
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49 for line in coverage( [g1, g2] ):
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50 if type( line ) is GenomicInterval:
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51 out_file.write( "%s\n" % "\t".join( line.fields ) )
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52 else:
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53 out_file.write( "%s\n" % line )
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4ef9819dc7fb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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54 except ParseError as exc:
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55 out_file.close()
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56 fail( "Invalid file format: %s" % str( exc ) )
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57
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58 out_file.close()
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59
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60 if g1.skipped > 0:
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4ef9819dc7fb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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61 print(skipped( g1, filedesc=" of 1st dataset" ))
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62 if g2.skipped > 0:
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4ef9819dc7fb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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63 print(skipped( g2, filedesc=" of 2nd dataset" ))
4ef9819dc7fb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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64
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65
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66 if __name__ == "__main__":
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67 main()