Mercurial > repos > yating-l > jbrowsearchivecreator

diff util/subtools.py @ 16:8bcec8dbb8be draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 0648e2769587d7fd544b3c6dacfa2b5c15a4c4a9
author yating-l
date Mon, 25 Jun 2018 15:39:39 -0400
parents 43a700afd457
children 315a40b0b694
line wrap: on
line diff
--- a/util/subtools.py	Wed Jun 20 17:43:26 2018 -0400
+++ b/util/subtools.py	Mon Jun 25 15:39:39 2018 -0400
@@ -294,10 +294,11 @@
         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(filteredFile.name, sortedFile)
+        gff3sort(inputFile, 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)