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1 #!/usr/bin/env python
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2 """
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3 Merge overlaping regions.
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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 -m, --mincols=N: Require this much overlap (default 1bp)
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8 -3, --threecol: Output 3 column bed
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9 """
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10 import sys, traceback, fileinput
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11 from warnings import warn
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12 from bx.intervals import *
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13 from bx.intervals.io import *
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14 from bx.intervals.operations.merge import *
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15 from bx.cookbook import doc_optparse
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16 from galaxy.tools.util.galaxyops import *
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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 def main():
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21 mincols = 1
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22 upstream_pad = 0
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23 downstream_pad = 0
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24
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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 if options.mincols: mincols = int( options.mincols )
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29 in_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
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40 out_file = open( out_fname, "w" )
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41
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42 try:
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43 for line in merge(g1,mincols=mincols):
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44 if options.threecol:
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45 if type( line ) is GenomicInterval:
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46 out_file.write( "%s\t%s\t%s\n" % ( line.chrom, str( line.startCol ), str( line.endCol ) ) )
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47 elif type( line ) is list:
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48 out_file.write( "%s\t%s\t%s\n" % ( line[chr_col_1], str( line[start_col_1] ), str( line[end_col_1] ) ) )
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49 else:
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50 out_file.write( "%s\n" % line )
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51 else:
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52 if type( line ) is GenomicInterval:
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53 out_file.write( "%s\n" % "\t".join( line.fields ) )
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54 elif type( line ) is list:
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55 out_file.write( "%s\n" % "\t".join( line ) )
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56 else:
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57 out_file.write( "%s\n" % line )
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58 except ParseError, exc:
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59 out_file.close()
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60 fail( "Invalid file format: %s" % str( exc ) )
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61
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62 out_file.close()
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63
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64 if g1.skipped > 0:
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65 print skipped( g1, filedesc=" of 1st dataset" )
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66
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67 if __name__ == "__main__":
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68 main()
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