--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/phytab_pal2nal.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+
+"""
+pal2nal.py
+----------
+Runs pal2nal.pl on GENENAME protein/DNA file pairings. Each file with protein
+    information must have a corresponding file with DNA information for its
+    gene. Depends on the Splitter class from splitterforpal2nal.py, which must
+    be in the same path as this script Designed for use with the Galaxy
+    bioinformatics platform. 
+"""
+
+import os
+import sys
+import zipfile
+import shutil
+from splitter import Splitter
+
+__author__ = 'William Chen'
+__license__ = 'BSD 2-clause'
+__status__ = 'In development'
+
+# declare working directory
+CDIR = '/home/galaxy/galaxy-dist/tools/Chen_dev/splitforpal2nal/'
+
+# get inputs for pal2nal.pl
+protFile = sys.argv[1] # Phytab file with protein info
+dnaFile = sys.argv[2] # Phytab file with DNA info 
+outputType = sys.argv[3]
+blockonly = sys.argv[4]
+nogap = sys.argv[5]
+nomismatch = sys.argv[6]
+codontable = sys.argv[7]
+outFormat = sys.argv[8]
+
+# remove whatever is at the file location marked as the output, if exists 
+try:
+    os.remove(sys.argv[9])
+except OSError:
+    pass
+# change working directory to where we want
+os.chdir(CDIR)
+# call Splitter from splitterforpal2nal.py and split the Phytab files into
+#  FASTA files
+sp = Splitter(dnaFile=dnaFile, protFile=protFile)
+sp.generateFasta()
+# create zip file to collect pal2nal.pl output
+zip = zipfile.ZipFile('myzip.zip', 'w')
+# run FASTA output through pal2nal.pl and write pal2nal.pl's output into a zip
+#  file
+# TODO: Use Popen instead of os.system
+for key in sp.getProteinInfo():
+    os.system('perl pal2nal.pl ' + key + 'Prot.fas ' + key + 'DNA.fas' + ' ' +
+              outputType + ' ' + blockonly + ' ' + nogap + ' ' + nomismatch +
+              ' ' +  codontable + ' -output ' + outFormat + ' 1> out' + key +
+              ' 2>/dev/null')
+    zip.write('out' + key)
+
+# move the zip file to the output location
+os.system('mv myzip.zip ' + sys.argv[9])
+
+# print the output location for reference
+print(sys.argv[9])