Mercurial > repos > yating-l > jbrowsearchivecreator

diff util/subtools.py @ 17:315a40b0b694 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 891eca7a697643c9b5365781bbab5b655972ffdc
author yating-l
date Mon, 25 Jun 2018 16:05:01 -0400
parents 8bcec8dbb8be
children 79b23a8afb15
line wrap: on
line diff
--- a/util/subtools.py	Mon Jun 25 15:39:39 2018 -0400
+++ b/util/subtools.py	Mon Jun 25 16:05:01 2018 -0400
@@ -294,11 +294,10 @@
         bedSort(inputFile, sortedFile)
     elif "gff" in dataType:
         fileType = 'gff'
-        #filteredFile = tempfile.NamedTemporaryFile(bufsize=0)
-        #remove_gene_lines(inputFile, filteredFile.name)
+        filteredFile = tempfile.NamedTemporaryFile(bufsize=0)
+        remove_gene_lines(inputFile, filteredFile.name)
         sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
-        #gff3sort(filteredFile.name, sortedFile)
-        gff3sort(inputFile, sortedFile)
+        gff3sort(filteredFile.name, sortedFile)
         # add .gff3.gz extension to Tabix GFF3 files, in order to enable creating name index with generate-names.pl
         trackName = trackName + '.gff3.gz'
     compressedFile = bgzip(sortedFile.name)