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bin/codonAlign.py

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+#!/usr/bin/env python
+# coding=utf-8
+
+__author__ = "Lin Dechun"
+__copyright__ = "Copyright 2016, BGI Research."
+__credits__ = ["Lin Dechun"]
+__version__ = "0.0.1"
+__maintainer__ = "Lin Dechun"
+__email__ = "[email protected]"
+
+from glob import glob
+from subprocess import Popen,PIPE
+from Bio import SeqIO
+import sys,os
+
+if len(sys.argv) != 3:
+    sys.exit("Usage: python {0} < the path of raw fasta, dir: *.fa> <output path>".format(sys.argv[0]))
+
+for i in glob(sys.argv[1]+'/*.fa'):
+    filename=os.path.basename(i)
+    Ofile=sys.argv[2]+'/'+filename
+
+    os.system('megacc -a '+os.path.dirname(os.path.realpath(__file__))+'/clustal_align_coding.mao -d '+i+' -o '+Ofile+' -f Fasta -n')
+    os.system('mv '+Ofile.replace('.fa','.fasta')+' '+Ofile)
+
+    record=[]
+    for line in SeqIO.parse(Ofile,'fasta'):
+        record.append(line)
+    SeqIO.write(record,open(Ofile,'w'),"fasta")