root/galaxy-central/tools/new_operations/gops_complement.py

#!/usr/bin/env python
"""
Complement regions.

usage: %prog in_file out_file
    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
    -l, --lengths=N: Filename of .len file for species (chromosome lengths)
    -a, --all: Complement all chromosomes (Genome-wide complement)
"""
from galaxy import eggs
import pkg_resources
pkg_resources.require( "bx-python" )
import sys, traceback, fileinput
from warnings import warn
from bx.intervals import *
from bx.intervals.io import *
from bx.intervals.operations.complement import complement
from bx.intervals.operations.subtract import subtract
from bx.cookbook import doc_optparse
from galaxy.tools.util.galaxyops import *

assert sys.version_info[:2] >= ( 2, 4 )

def main():
    allchroms = False
    upstream_pad = 0
    downstream_pad = 0

    options, args = doc_optparse.parse( __doc__ )
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
        lengths = options.lengths
        if options.all: allchroms = True
        in_fname, out_fname = args
    except:
        doc_optparse.exception()

    g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
                            chrom_col=chr_col_1,
                            start_col=start_col_1,
                            end_col=end_col_1,
                            strand_col=strand_col_1,
                            fix_strand=True )

    lens = dict()
    chroms = list()
    # dbfile is used to determine the length of each chromosome.  The lengths
    # are added to the lens dict and passed copmlement operation code in bx.
    dbfile = fileinput.FileInput( lengths )
    
    if dbfile:
        if not allchroms:
            try:
                for line in dbfile:
                    fields = line.split("\t")
                    lens[fields[0]] = int(fields[1])
            except:
                # assume LEN doesn't exist or is corrupt somehow
                pass
        elif allchroms:
            try:
                for line in dbfile:
                    fields = line.split("\t")
                    end = int(fields[1])
                    chroms.append("\t".join([fields[0],"0",str(end)]))
            except:
                pass

    # Safety...if the dbfile didn't exist and we're on allchroms, then
    # default to generic complement
    if allchroms and len(chroms) == 0:
        allchroms = False

    if allchroms:
        chromReader = GenomicIntervalReader(chroms)
        generator = subtract([chromReader, g1])
    else:
        generator = complement(g1, lens)

    out_file = open( out_fname, "w" )

    try:
        for interval in generator:
            if type( interval ) is GenomicInterval:
                out_file.write( "%s\n" % "\t".join( interval ) )
            else:
                out_file.write( "%s\n" % interval )
    except ParseError, exc:
        out_file.close()
        fail( "Invalid file format: %s" % str( exc ) )

    out_file.close()

    if g1.skipped > 0:
        print skipped( g1, filedesc="" )

if __name__ == "__main__":
    main()