Mercurial > repos > rnateam > graphclust_preprocessing

diff splitSHAPE.py @ 11:c0c9d19bc7b2 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
author rnateam
date Tue, 18 Jul 2017 01:43:49 -0400
parents 0690d59881b9
children
line wrap: on
line diff
--- a/splitSHAPE.py	Thu Jun 01 12:11:37 2017 -0400
+++ b/splitSHAPE.py	Tue Jul 18 01:43:49 2017 -0400
@@ -3,7 +3,6 @@
 import sys
 
 shape_file = sys.argv[1]
-win_size = int(sys.argv[2])
 
 pattern = re.compile("^>.*$")
 toWrite = ""
@@ -18,9 +17,9 @@
 name_file = "FASTA/data.names"
 array_all_chunks = []
 with open(name_file, 'r') as f:
-    content = f.read()
-    lines = content.split('\n')[:-1]
-    for line in lines:
+    for line in f:
+        if len(line.strip()) == 0:
+            continue
         seq_id.append(int(line.split()[0]))
         seq_string.append(line.split()[1])
         orig_id_srt = line.split()[3]