Removed the output option, enahcned the README.

README

@@ -19,17 +19,17 @@ Now our scripts are dockerized and we can use it directly from the image.
 
 # Push our image to the SevenBridges registry
 
-First we need to tag the image
+First we need to tag the image. Make sure you have create a dev project called `dna2protein`, otherwise you will
+not be able to push the image.
 
 	docker tag mmattioni/dna2protein images.sbgenomics.com/mmattioni/dna2protein
 
-Now we login and push it to the registry
+Now we login and push it to the registry. Note: you have to provide you API TOKEN, not the password you use to log 
+on the Seven Bridges Platform.
 
 	docker login --username <SBG_USERNAME> --email <SBG_EMAIL> --password <SBG_API_TOKEN> images.sbgenomics.com
 	docker push mmattioni/dna2protein
 
-
-
 
 
 

transcribe.py

@@ -3,7 +3,8 @@
 import re
 import sys
 
-VERSION = "0.5.1"
+VERSION = "0.5.2.dev"
+FILENAME_OUTPUT = "rna.txt"
 
 def transcribe(args):
 	# create a transcription map and use regex to translate
@@ -15,17 +16,16 @@ def transcribe(args):
 
 	print "Welcome to transcribe, version: {0}".format(VERSION)
 	if args['verbose']:
-		print ("Your original DNA sequence: {0}".format(DNA))
-		print ("Your translated mRNA sequence: {0}".format(mRNA))
-	with open(args['output'], "w") as output:
+		print "mRNA has been translated. Result in {0}".format(FILENAME_OUTPUT)
+	with open(FILENAME_OUTPUT, "w") as output:
 		output.write(mRNA)
+	print "Done."
 
 if __name__ == "__main__":
 	""" Parse the command line arguments """
 	parser = argparse.ArgumentParser(description="Translates a DNA input test into a RNA", 
 									formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 	parser.add_argument("dna", type=argparse.FileType("r"))
-	parser.add_argument("--output", "-o", default="rna.txt")
 	parser.add_argument("-v", "--verbose", action="store_true", default=False)
 	parser.add_argument("--version", action='version', version=VERSION) 
 	args = vars(parser.parse_args())

translate.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 import argparse
-import sys
 from transcribe import VERSION
 
+FILENAME_OUTPUT = "peptide.txt"
+
 def translate(args):
 
     print "Welcome to translate, version: {0}".format(VERSION)
@@ -32,22 +33,22 @@ def translate(args):
             protein += codon_map[mRNA[start:start+3]]
             start += 3
         protein = protein[:protein.find('STOP')]
-        with open(args['output'], "w") as output:
+        with open(FILENAME_OUTPUT, "w") as output:
             output.write(protein)
             if args['verbose']:
-                print "Protein has been transcribed. Result in {0}".format(args['output'])
+                print "Protein has been transcribed. Result in {0}".format(FILENAME_OUTPUT)
+
     else:
         msg = "No AUG found as starting codon in your mRNA input. This program translates only mRNA "
         msg += "from eukaryotes: https://en.wikipedia.org/wiki/Start_codon"
         print msg
-        
+    print "Done."
 
 if __name__ == "__main__":
     """ Parse the command line arguments """
     parser = argparse.ArgumentParser(description="Transcribe the provided mRNA into a peptide.", 
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument("mRNA", type=argparse.FileType('r'), help="mRNA to transcribe")
-    parser.add_argument("--output", "-o", default="peptide.txt")
     parser.add_argument("--verbose", "-v", help="Run in verbose mode", action="store_true")
     parser.add_argument("--version", action='version', version=VERSION)
     args = vars(parser.parse_args())