Mercurial > repos > dfornika > match_plasmid_to_reference

diff match_plasmid_to_reference.py @ 1:3616b6eda1da draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 00:42:05 -0500
parents 8bb674372911
children 826ddf832bef
line wrap: on
line diff
--- a/match_plasmid_to_reference.py	Wed Nov 06 00:08:43 2019 -0500
+++ b/match_plasmid_to_reference.py	Wed Nov 06 00:42:05 2019 -0500
@@ -65,18 +65,22 @@
             if line.startswith('ACCESSION'):
                 return line.strip().split()[1]
 
-            
 
 def count_contigs(plasmid_fasta_path):
     contigs = 0
     with open(plasmid_fasta_path, 'r') as f:
-        contigs = 2
+        for line in f:
+            if line.startswith('>'):
+                contigs += 1
     return contigs
 
 def count_bases(plasmid_fasta_path):
     bases = 0
     with open(plasmid_fasta_path, 'r') as f:
-        bases = 11117
+        for line in f:
+            line = line.strip()
+            if not line.startswith('>'):
+                bases += len(line)
     return bases
 
 def main(args):