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changeset 31:3cb2af2435d3 draft

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Uploaded
author gianmarco_piccinno
date Wed, 12 Dec 2018 08:48:22 -0500
parents e12061ce9601
children 02503b9c8c39
files codon_usage.py codon_usage.xml
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/codon_usage.py	Wed Dec 12 08:23:56 2018 -0500
+++ b/codon_usage.py	Wed Dec 12 08:48:22 2018 -0500
@@ -9,7 +9,6 @@
 import sys
 import os
 import pandas as pd
-#from BCBio import GFF
 
 
 def read_input(data = "example.fna", type_ = "fasta"):
@@ -143,7 +142,7 @@
     seqs = read_input(data=args['input'], type_=args['type'])
     out = codon_usage(seqs, args['codonTable'])
 
-    with open(args['output'], "w") as outf:
+    with open(args['output']+".csv", "w") as outf:
         out["Table"].to_csv(outf, sep="\t", index_label=["AA", "Codon"])
 
     
\ No newline at end of file
--- a/codon_usage.xml	Wed Dec 12 08:23:56 2018 -0500
+++ b/codon_usage.xml	Wed Dec 12 08:48:22 2018 -0500
@@ -5,6 +5,7 @@
     <requirement type="package" version="2.7.15">python</requirement>
     <requirement type="package" version="1.72">biopython</requirement>
     <requirement type="package" version="0.23.4">pandas</requirement>
+    <requirement type="package" version="1.15.3">numpy</requirement>
   </requirements> 
   
   <command>