# HG changeset patch
# User dfornika
# Date 1573018925 18000
# Node ID 3616b6eda1dab84e45446e38dc7d4340dedfb7ea
# Parent 8bb674372911ba0431b5a4696c2e18e43304b6ed
"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
diff -r 8bb674372911 -r 3616b6eda1da match_plasmid_to_reference.py
--- 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):
diff -r 8bb674372911 -r 3616b6eda1da match_plasmid_to_reference.xml
--- a/match_plasmid_to_reference.xml Wed Nov 06 00:08:43 2019 -0500
+++ b/match_plasmid_to_reference.xml Wed Nov 06 00:42:05 2019 -0500
@@ -19,10 +19,23 @@
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