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1 #!/usr/bin/env python
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2 """
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3 Complement 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 chrom, start, end, strand in file
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7 -l, --lengths=N: Filename of .len file for species (chromosome lengths)
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8 -a, --all: Complement all chromosomes (Genome-wide complement)
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9 """
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10 from galaxy import eggs
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11 import pkg_resources
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12 pkg_resources.require( "bx-python" )
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13 import sys, traceback, fileinput
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14 from warnings import warn
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15 from bx.intervals import *
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16 from bx.intervals.io import *
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17 from bx.intervals.operations.complement import complement
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18 from bx.intervals.operations.subtract import subtract
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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 allchroms = False
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26 upstream_pad = 0
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27 downstream_pad = 0
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28
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29 options, args = doc_optparse.parse( __doc__ )
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30 try:
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31 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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32 lengths = options.lengths
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33 if options.all: allchroms = True
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34 in_fname, out_fname = args
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35 except:
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36 doc_optparse.exception()
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37
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38 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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39 chrom_col=chr_col_1,
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40 start_col=start_col_1,
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41 end_col=end_col_1,
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42 strand_col=strand_col_1,
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43 fix_strand=True )
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44
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45 lens = dict()
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46 chroms = list()
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47 # dbfile is used to determine the length of each chromosome. The lengths
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48 # are added to the lens dict and passed copmlement operation code in bx.
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49 dbfile = fileinput.FileInput( lengths )
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50
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51 if dbfile:
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52 if not allchroms:
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53 try:
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54 for line in dbfile:
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55 fields = line.split("\t")
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56 lens[fields[0]] = int(fields[1])
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57 except:
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58 # assume LEN doesn't exist or is corrupt somehow
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59 pass
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60 elif allchroms:
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61 try:
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62 for line in dbfile:
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63 fields = line.split("\t")
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64 end = int(fields[1])
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65 chroms.append("\t".join([fields[0],"0",str(end)]))
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66 except:
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67 pass
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68
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69 # Safety...if the dbfile didn't exist and we're on allchroms, then
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70 # default to generic complement
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71 if allchroms and len(chroms) == 0:
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72 allchroms = False
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73
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74 if allchroms:
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75 chromReader = GenomicIntervalReader(chroms)
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76 generator = subtract([chromReader, g1])
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77 else:
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78 generator = complement(g1, lens)
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79
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80 out_file = open( out_fname, "w" )
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81
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82 try:
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83 for interval in generator:
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84 if type( interval ) is GenomicInterval:
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85 out_file.write( "%s\n" % "\t".join( interval ) )
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86 else:
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87 out_file.write( "%s\n" % interval )
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88 except ParseError, exc:
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89 out_file.close()
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90 fail( "Invalid file format: %s" % str( exc ) )
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91
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92 out_file.close()
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93
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94 if g1.skipped > 0:
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95 print skipped( g1, filedesc="" )
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96
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97 if __name__ == "__main__":
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98 main()
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