/tools/new_operations/gops_cluster.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 132 lines · 101 code · 13 blank · 18 comment · 34 complexity · 4c056b62a5b4d01487f1260d90d3ba50 MD5 · raw file
- #!/usr/bin/env python
- """
- Cluster regions of intervals.
- usage: %prog in_file out_file
- -1, --cols1=N,N,N,N: Columns for start, end, strand in file
- -d, --distance=N: Maximum distance between clustered intervals
- -v, --overlap=N: Minimum overlap require (negative distance)
- -m, --minregions=N: Minimum regions per cluster
- -o, --output=N: 1)merged 2)filtered 3)clustered 4) minimum 5) maximum
- """
- 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.find_clusters import *
- from bx.cookbook import doc_optparse
- from galaxy.tools.util.galaxyops import *
- assert sys.version_info[:2] >= ( 2, 4 )
- def main():
- distance = 0
- minregions = 2
- output = 1
- 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 )
- if options.distance: distance = int( options.distance )
- if options.overlap: distance = -1 * int( options.overlap )
- if options.output: output = int( options.output )
- if options.minregions: minregions = int( options.minregions )
- 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 )
- # Get the cluster tree
- try:
- clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
- except ParseError, exc:
- fail( "Invalid file format: %s" % str( exc ) )
- f1 = open( in_fname, "r" )
- out_file = open( out_fname, "w" )
-
- # If "merge"
- if output == 1:
- fields = ["." for x in range(max(g1.chrom_col, g1.start_col, g1.end_col)+1)]
- for chrom, tree in clusters.items():
- for start, end, lines in tree.getregions():
- fields[g1.chrom_col] = chrom
- fields[g1.start_col] = str(start)
- fields[g1.end_col] = str(end)
- out_file.write( "%s\n" % "\t".join( fields ) )
- # If "filtered" we preserve order of file and comments, etc.
- if output == 2:
- linenums = dict()
- for chrom, tree in clusters.items():
- for linenum in tree.getlines():
- linenums[linenum] = 0
- linenum = -1
- f1.seek(0)
- for line in f1.readlines():
- linenum += 1
- if linenum in linenums or linenum in extra:
- out_file.write( "%s\n" % line.rstrip( "\n\r" ) )
- # If "clustered" we output original intervals, but near each other (i.e. clustered)
- if output == 3:
- linenums = list()
- f1.seek(0)
- fileLines = f1.readlines()
- for chrom, tree in clusters.items():
- for linenum in tree.getlines():
- out_file.write( "%s\n" % fileLines[linenum].rstrip( "\n\r" ) )
- # If "minimum" we output the smallest interval in each cluster
- if output == 4 or output == 5:
- linenums = list()
- f1.seek(0)
- fileLines = f1.readlines()
- for chrom, tree in clusters.items():
- regions = tree.getregions()
- for start, end, lines in tree.getregions():
- outsize = -1
- outinterval = None
- for line in lines:
- # three nested for loops?
- # should only execute this code once per line
- fileline = fileLines[line].rstrip("\n\r")
- try:
- cluster_interval = GenomicInterval( g1, fileline.split("\t"),
- g1.chrom_col,
- g1.start_col,
- g1.end_col,
- g1.strand_col,
- g1.default_strand,
- g1.fix_strand )
- except Exception, exc:
- print >> sys.stderr, str( exc )
- f1.close()
- sys.exit()
- interval_size = cluster_interval.end - cluster_interval.start
- if outsize == -1 or \
- ( outsize > interval_size and output == 4 ) or \
- ( outsize < interval_size and output == 5 ) :
- outinterval = cluster_interval
- outsize = interval_size
- out_file.write( "%s\n" % outinterval )
- f1.close()
- out_file.close()
-
- if g1.skipped > 0:
- print skipped( g1, filedesc="" )
- if __name__ == "__main__":
- main()