Mercurial > repos > bornea > filter_fasta

changeset 5:af454e5a9ef5 draft

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Uploaded
author bornea
date Sat, 06 Aug 2016 17:00:41 -0400
parents 489b560129c8
children 5990c4dbfbaa
files filter_fasta.py
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/filter_fasta.py	Sat Aug 06 16:57:14 2016 -0400
+++ b/filter_fasta.py	Sat Aug 06 17:00:41 2016 -0400
@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+
 """
 Python-code: Merge Scaffold Samples Report files
 @author = Brent Kuenzi
@@ -22,6 +22,7 @@
             line = line.strip()
             temp = line.split('\t')
             output.append(temp)
+            print temp
     return output
 def getAccessions(infile): # get list of protein accessions from your data
     data = readtab(infile)
@@ -82,6 +83,7 @@
     with open("output.fasta","wt") as x:
         for i in header:
             x.write(i+'\n'+seq[cnt]+'\n')
+            print i+'\n'+seq[cnt]+'\n'
             cnt+=1
 fasta = sys.argv[1] # fasta file to filter
 data = sys.argv[2] # scaffold report #2 -- filename