root/galaxy-central/tools/regVariation/windowSplitter.py

#!/usr/bin/env python

"""
Split into windows.

usage: %prog input size out_file
   -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
"""

import sys, re, os

from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse
from galaxy.tools.util.galaxyops import *

def stop_err( msg ):
    sys.stderr.write( msg )
    sys.exit()

def main():   
    # Parsing Command Line here
    options, args = doc_optparse.parse( __doc__ )
    
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
        inp_file, winsize, out_file, makesliding, offset = args
        winsize = int(winsize)
        offset = int(offset)
        makesliding = int(makesliding)
        if strand_col_1 <= 0:
            strand = "+"        #if strand is not defined, default it to +
    except:
        stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." )
    
    fo = open(out_file,'w')

    skipped_lines = 0
    first_invalid_line = 0
    invalid_line = None
    if offset == 0:
        makesliding = 0

    for i, line in enumerate( file( inp_file ) ):
        line = line.strip()
        if line and line[0:1] != "#":
            try:
                elems = line.split('\t')
                if strand_col_1 != -1:
                    strand = elems[strand_col_1]
                start = int(elems[start_col_1])
                end = int(elems[end_col_1])
                if makesliding == 0:
                    numwin = (end - start)/winsize
                else:
                    numwin = (end - start)/offset
                if numwin > 0:
                    for win in range(numwin):
                        elems_1 = elems
                        elems_1[start_col_1] = str(start)
                        elems_1[end_col_1] = str(start + winsize)
                        fo.write( "%s\n" % '\t'.join( elems_1 ) )
                        if makesliding == 0:
                            start = start + winsize
                        else:
                            start = start + offset
                            if start+winsize > end:
                                break
            except:
                skipped_lines += 1
                if not invalid_line:
                    first_invalid_line = i + 1
                    invalid_line = line
    
    fo.close()

    if makesliding == 1:                
        print 'Window size=%d, Sliding=Yes, Offset=%d' %(winsize, offset)
    else:
        print 'Window size=%d, Sliding=No' %(winsize)
    if skipped_lines > 0:
        print 'Skipped %d invalid lines starting with #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )             
    
if __name__ == "__main__":
    main()