diff gops_merge.py @ 0:10ac6097acdb

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gops_merge.py	Tue Apr 01 09:13:25 2014 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+"""
+Merge overlaping regions.
+
+usage: %prog in_file out_file
+    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
+    -m, --mincols=N: Require this much overlap (default 1bp)
+    -3, --threecol: Output 3 column bed
+"""
+import sys, traceback, fileinput
+from warnings import warn
+from bx.intervals import *
+from bx.intervals.io import *
+from bx.intervals.operations.merge import *
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    mincols = 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.mincols: mincols = int( options.mincols )
+        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 )
+
+    out_file = open( out_fname, "w" )
+
+    try:
+        for line in merge(g1,mincols=mincols):
+            if options.threecol:
+                if type( line ) is GenomicInterval:
+                    out_file.write( "%s\t%s\t%s\n" % ( line.chrom, str( line.startCol ), str( line.endCol ) ) )
+                elif type( line ) is list:
+                    out_file.write( "%s\t%s\t%s\n" % ( line[chr_col_1], str( line[start_col_1] ), str( line[end_col_1] ) ) )
+                else:
+                    out_file.write( "%s\n" % line )
+            else:
+                if type( line ) is GenomicInterval:
+                    out_file.write( "%s\n" % "\t".join( line.fields ) )
+                elif type( line ) is list:
+                    out_file.write( "%s\n" % "\t".join( line ) )
+                else:
+                    out_file.write( "%s\n" % line )
+    except ParseError, exc:
+        out_file.close()
+        fail( "Invalid file format: %s" % str( exc ) )
+
+    out_file.close()
+
+    if g1.skipped > 0:
+        print skipped( g1, filedesc=" of 1st dataset" )
+
+if __name__ == "__main__":
+    main()