Mercurial > repos > devteam > cluster
view gops_cluster.py @ 4:05696474ee89 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author | devteam |
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date | Thu, 22 Jun 2017 18:40:19 -0400 |
parents | 765ceb06c3e2 |
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#!/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 __future__ import print_function import fileinput import sys from bx.cookbook import doc_optparse from bx.intervals.io import GenomicInterval, NiceReaderWrapper from bx.intervals.operations.find_clusters import find_clusters from bx.tabular.io import ParseError from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped assert sys.version_info[:2] >= ( 2, 4 ) def main(): distance = 0 minregions = 2 output = 1 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 as 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(): 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 as exc: print(str( exc ), file=sys.stderr) 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()