Mercurial > repos > yating-l > rename_scaffolds

diff rename.py @ 1:148e353417e7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit af6c4dc7f6d6795f2b2db7299eb14ae1d5622ac1
author yating-l
date Fri, 30 Dec 2016 17:50:54 -0500
parents 1a0e39acb62f
children
line wrap: on
line diff
--- a/rename.py	Mon Dec 19 17:14:55 2016 -0500
+++ b/rename.py	Fri Dec 30 17:50:54 2016 -0500
@@ -14,13 +14,17 @@
                 if ">" in line:
                     oldname = line[1:].rstrip()
                     newname = "scaffold_" + str(i)
-                    line = ">" + newname + "\n"
+                    line = ">" + newname
                     i = i+1
                     namemap[oldname] = newname
-                out.write(line)
+                #TODO: Add line breaks to chromosome sequences that are in a single line
+                #else:
+                    #if (len(line) > 50):
+                        #for 
+                out.write(line.rstrip() + "\n")
     with open(indexfile, 'w') as index:
         for k in namemap:
-            index.write(k + "=>" + namemap[k] + "\n")
+            index.write(k + "\t" + namemap[k] + "\n")
 
 def main():
     inputfile = str(sys.argv[1])