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1 #!/usr/bin/env python
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2 """
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3 Count total base coverage.
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4
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5 usage: %prog in_file out_file
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6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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7 """
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8
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9 import sys, traceback, fileinput
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10 from warnings import warn
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11 from bx.intervals import *
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12 from bx.intervals.io import *
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13 from bx.intervals.operations.base_coverage import *
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14 from bx.cookbook import doc_optparse
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15 from galaxy.tools.util.galaxyops import *
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16
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17 assert sys.version_info[:2] >= ( 2, 4 )
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18
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19 def main():
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20 upstream_pad = 0
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21 downstream_pad = 0
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22
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23 options, args = doc_optparse.parse( __doc__ )
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24 try:
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25 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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26 in_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
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37 try:
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38 bases = base_coverage(g1)
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39 except ParseError, exc:
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40 fail( "Invalid file format: %s" % str( exc ) )
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41 out_file = open( out_fname, "w" )
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42 out_file.write( "%s\n" % str( bases ) )
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43 out_file.close()
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44 if g1.skipped > 0:
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45 print skipped( g1, filedesc="" )
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46
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47 if __name__ == "__main__":
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48 main()
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