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1 #!/usr/bin/env python
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2 """
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3 Join two sets of intervals using their overlap as the key.
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4
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5 usage: %prog bed_file_1 bed_file_2 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 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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8 -m, --mincols=N: Require this much overlap (default 1bp)
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9 -f, --fill=N: none, right, left, both
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10 """
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11 from galaxy import eggs
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12 import pkg_resources
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13 pkg_resources.require( "bx-python" )
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14 import sys, traceback, fileinput
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15 from warnings import warn
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16 from bx.intervals import *
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17 from bx.intervals.io import *
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18 from bx.intervals.operations.join import *
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19 from bx.cookbook import doc_optparse
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20 from galaxy.tools.util.galaxyops import *
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21
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22 assert sys.version_info[:2] >= ( 2, 4 )
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23
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24 def main():
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25 mincols = 1
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26 upstream_pad = 0
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27 downstream_pad = 0
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28 leftfill = False
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29 rightfill = False
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30
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31 options, args = doc_optparse.parse( __doc__ )
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32 try:
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33 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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34 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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35 if options.mincols: mincols = int( options.mincols )
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36 if options.fill:
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37 if options.fill == "both":
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38 rightfill = leftfill = True
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39 else:
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40 rightfill = options.fill == "right"
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41 leftfill = options.fill == "left"
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42 in_fname, in2_fname, out_fname = args
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43 except:
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44 doc_optparse.exception()
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45
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46 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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47 chrom_col=chr_col_1,
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48 start_col=start_col_1,
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49 end_col=end_col_1,
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50 strand_col=strand_col_1,
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51 fix_strand=True )
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52 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
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53 chrom_col=chr_col_2,
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54 start_col=start_col_2,
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55 end_col=end_col_2,
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56 strand_col=strand_col_2,
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57 fix_strand=True )
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58
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59 out_file = open( out_fname, "w" )
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60
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61 try:
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62 for outfields in join(g1, g2, mincols=mincols, rightfill=rightfill, leftfill=leftfill):
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63 if type( outfields ) is list:
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64 out_file.write( "%s\n" % "\t".join( outfields ) )
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65 else:
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66 out_file.write( "%s\n" % outfields )
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67 except ParseError, exc:
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68 out_file.close()
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69 fail( "Invalid file format: %s" % str( exc ) )
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70 except MemoryError:
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71 out_file.close()
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72 fail( "Input datasets were too large to complete the join operation." )
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73
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74 out_file.close()
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75
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76 if g1.skipped > 0:
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77 print skipped( g1, filedesc=" of 1st dataset" )
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78 if g2.skipped > 0:
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79 print skipped( g2, filedesc=" of 2nd dataset" )
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80
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81 if __name__ == "__main__":
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82 main()
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