From 124f0e8adfe7b829cb160e613c671d51dec2d8ea Mon Sep 17 00:00:00 2001
From: free hacker <freeh4cker@gmail.com>
Date: Thu, 18 Feb 2016 08:19:13 +0100
Subject: [PATCH] add gc_percent in Sequence and use it
---
source/_static/code/fasta_object.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/source/_static/code/fasta_object.py b/source/_static/code/fasta_object.py
index a1a32c8..abb474a 100644
--- a/source/_static/code/fasta_object.py
+++ b/source/_static/code/fasta_object.py
@@ -5,6 +5,9 @@ class Sequence(object):
self.comment = comment
self.sequence = sequence
+ def gc_percent(self):
+ seq = self.sequence.upper()
+ return float(seq.count('G') + seq.count('C')) / float(len(seq))
class FastaParser(object):
@@ -73,4 +76,5 @@ if __name__ == '__main__':
fasta_parser = FastaParser(fasta_path)
for sequence in fasta_parser:
print "----------------"
- print sequence.id
\ No newline at end of file
+ print "{seqid} = {gc:.3%}".format(gc=sequence.gc_percent(),
+ seqid = sequence.id)
\ No newline at end of file
--
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