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annotate gops_coverage.py @ 2:7b226a8a6722 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:50:01 -0400
parents 6b81ee6c18d3
children ad25eb2c422d
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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 """
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10 import fileinput
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11 import sys
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12 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
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13 from bx.intervals.operations.coverage import coverage
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14 from bx.cookbook import doc_optparse
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15 from bx.tabular.io import ParseError
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16 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
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17
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18 assert sys.version_info[:2] >= ( 2, 4 )
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19
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20
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21 def main():
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22 options, args = doc_optparse.parse( __doc__ )
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23 try:
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24 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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25 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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26 in_fname, in2_fname, out_fname = args
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27 except:
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28 doc_optparse.exception()
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29
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30 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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31 chrom_col=chr_col_1,
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32 start_col=start_col_1,
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33 end_col=end_col_1,
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34 strand_col=strand_col_1,
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35 fix_strand=True )
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36 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
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37 chrom_col=chr_col_2,
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38 start_col=start_col_2,
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39 end_col=end_col_2,
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40 strand_col=strand_col_2,
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41 fix_strand=True )
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42
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43 out_file = open( out_fname, "w" )
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44
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45 try:
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46 for line in coverage( [g1, g2] ):
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47 if type( line ) is GenomicInterval:
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48 out_file.write( "%s\n" % "\t".join( line.fields ) )
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49 else:
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50 out_file.write( "%s\n" % line )
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51 except ParseError, exc:
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52 out_file.close()
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53 fail( "Invalid file format: %s" % str( exc ) )
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54
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55 out_file.close()
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56
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57 if g1.skipped > 0:
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58 print skipped( g1, filedesc=" of 1st dataset" )
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59 if g2.skipped > 0:
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60 print skipped( g2, filedesc=" of 2nd dataset" )
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61
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62 if __name__ == "__main__":
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63 main()