Mercurial > repos > bornea > filter_fasta

changeset 11:573c36ff075f draft

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Uploaded
author bornea
date Tue, 16 Aug 2016 20:40:19 -0400
parents c9e6e2e7697c
children 05d48b118f81
files filter_fasta.py
diffstat 1 files changed, 2 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/filter_fasta.py	Tue Aug 16 20:36:24 2016 -0400
+++ b/filter_fasta.py	Tue Aug 16 20:40:19 2016 -0400
@@ -84,10 +84,8 @@
         x.write(i+'\n'+seq[cnt]+'\n')
         cnt+=1
     x.close()
-#fasta = sys.argv[1] # fasta file to filter
-#data = sys.argv[2] # scaffold report #2 -- filename
-fasta = r"C:\Users\Owner\Desktop\APOSTL\SAINT_preprocessing\SwissProt_HUMAN_2014_08.fasta"
-data = r"C:\Users\Owner\Desktop\APOSTL\Scaffold\scaffold_EGFR.txt"
+fasta = sys.argv[1] # fasta file to filter
+data = sys.argv[2] # scaffold report #2 -- filename
 
 FilterFastaSeq(fasta,getAccessions(data))
 os.rename("output.txt", "output1.txt")
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