diff gops_merge.py @ 3:b9c97d3233bb draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/gops_merge.py	Mon Apr 14 09:24:27 2014 -0400
+++ b/gops_merge.py	Tue Oct 13 12:51:07 2015 -0400
@@ -7,25 +7,25 @@
     -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 *
+import fileinput
+import sys
+from bx.intervals.io import GenomicInterval, NiceReaderWrapper
+from bx.intervals.operations.merge import merge
 from bx.cookbook import doc_optparse
-from galaxy.tools.util.galaxyops import *
+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():
     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 )
+        if options.mincols:
+            mincols = int( options.mincols )
         in_fname, out_fname = args
     except:
         doc_optparse.exception()
@@ -34,13 +34,13 @@
                             chrom_col=chr_col_1,
                             start_col=start_col_1,
                             end_col=end_col_1,
-                            strand_col = strand_col_1,
+                            strand_col=strand_col_1,
                             fix_strand=True )
 
     out_file = open( out_fname, "w" )
 
     try:
-        for line in merge(g1,mincols=mincols):
+        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 ) ) )