diff tools/new_operations/gops_concat.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/new_operations/gops_concat.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+"""
+Concatenate two bed files.  The concatenated files are returned in the
+same format as the first.  If --sameformat is specified, then all
+columns will be treated as the same, and all fields will be saved,
+although the output will be trimmed to match the primary input.  In
+addition, if --sameformat is specified, missing fields will be padded
+with a period(.).
+
+usage: %prog in_file_1 in_file_2 out_file
+    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in first file
+    -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in second file
+    -s, --sameformat: All files are precisely the same format.
+"""
+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.concat import *
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    sameformat=False
+    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 )
+        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
+        if options.sameformat: sameformat = True
+        in_file_1, in_file_2, out_fname = args
+    except:
+        doc_optparse.exception()
+
+    g1 = NiceReaderWrapper( fileinput.FileInput( in_file_1 ),
+                            chrom_col=chr_col_1,
+                            start_col=start_col_1,
+                            end_col=end_col_1,
+                            fix_strand=True )
+
+    g2 = NiceReaderWrapper( fileinput.FileInput( in_file_2 ),
+                            chrom_col=chr_col_2,
+                            start_col=start_col_2,
+                            end_col=end_col_2,
+                            strand_col=strand_col_2,
+                            fix_strand=True )
+
+    if strand_col_1 >= 0:
+        g1.strand_col = strand_col_1
+
+    out_file = open( out_fname, "w" )
+
+    try:
+        for line in concat( [g1, g2], sameformat=sameformat ):
+            if type( line ) is GenomicInterval:
+                out_file.write( "%s\n" % "\t".join( line.fields ) )
+            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 g2.skipped > 0:
+        print skipped( g2, filedesc=" of 2nd dataset" )
+        
+if __name__ == "__main__":
+    main()