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86 lines
2.8 KiB
Python
86 lines
2.8 KiB
Python
#!/usr/bin/env python
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"""
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Split into windows.
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usage: %prog input size out_file
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-l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
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"""
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import sys, re, os
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from galaxy import eggs
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import pkg_resources; pkg_resources.require( "bx-python" )
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from bx.cookbook import doc_optparse
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from galaxy.tools.util.galaxyops import *
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def main():
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# Parsing Command Line here
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options, args = doc_optparse.parse( __doc__ )
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try:
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chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
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inp_file, winsize, out_file, makesliding, offset = args
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winsize = int(winsize)
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offset = int(offset)
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makesliding = int(makesliding)
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if strand_col_1 <= 0:
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strand = "+" #if strand is not defined, default it to +
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except:
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stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." )
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fo = open(out_file,'w')
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skipped_lines = 0
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first_invalid_line = 0
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invalid_line = None
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if offset == 0:
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makesliding = 0
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for i, line in enumerate( file( inp_file ) ):
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line = line.strip()
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if line and line[0:1] != "#":
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try:
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elems = line.split('\t')
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if strand_col_1 != -1:
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strand = elems[strand_col_1]
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start = int(elems[start_col_1])
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end = int(elems[end_col_1])
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if makesliding == 0:
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numwin = (end - start)/winsize
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else:
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numwin = (end - start)/offset
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if numwin > 0:
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for win in range(numwin):
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elems_1 = elems
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elems_1[start_col_1] = str(start)
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elems_1[end_col_1] = str(start + winsize)
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fo.write( "%s\n" % '\t'.join( elems_1 ) )
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if makesliding == 0:
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start = start + winsize
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else:
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start = start + offset
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if start+winsize > end:
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break
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except:
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skipped_lines += 1
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if not invalid_line:
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first_invalid_line = i + 1
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invalid_line = line
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fo.close()
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if makesliding == 1:
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print 'Window size=%d, Sliding=Yes, Offset=%d' %(winsize, offset)
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else:
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print 'Window size=%d, Sliding=No' %(winsize)
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if skipped_lines > 0:
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print 'Skipped %d invalid lines starting with #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
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if __name__ == "__main__":
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main()
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