Added ability to read input from Quoll.

Author: icwells

bin/01_SplitFasta.py

@@ -87,6 +87,11 @@ def convertHeader(line):
 			# NCBI IDs
 			build = ">" + str(genebuild[2]) + "\n"
 			geneid = str(genebuild[0]) + "_" + str(genebuild[1])
+	elif "TRINITY" in line:
+		line = line.split("TRINITY-")[1]
+		line = line.strip()
+		build = ">" + line[:line.find("-")] + "\n"
+		geneid = line[line.find("-")+1:]
 	else:
 		# Extract build and geneid 
 		build = ">" + line.split(".")[0][1:].rstrip() + "\n"

bin/02_FilterFasta.py

@@ -94,19 +94,22 @@ def seqDict(fasta, n):
 def checkFrame(seqs, ref):
 	'''Removes gaps in the reference sequence introduced by
 	alignment and removes corresponding sites in other species'''
-	for codon in seqs[ref]: 
+	for idx,codon in enumerate(seqs[ref]): 
 		if codon == "---":
 			pass
 		else:
 			if "-" in str(codon):
 				# Remove gaps from reference sequence
 				i = codon.index("-")
-				idx = seqs[ref].index(codon)
 				codon = codon[:i] + codon[i + 1:]
 				for key in seqs:
-					# Remove corresponding gaps in other sequences
-					triplet = seqs[key][idx]
-					triplet = triplet[:i] + triplet[i + 1:]
+					if key != ref:
+						# Remove corresponding gaps in other sequences
+						try:
+							triplet = seqs[key][idx]
+							triplet = triplet[:i] + triplet[i + 1:]
+						except:
+							pass
 	return True, seqs
 
 def fixCodons(newseq):

bin/04_CallKaKs.py

@@ -24,8 +24,8 @@ def calculateKaKs(indir, outdir, method, axt):
 		filename = axt.split("/")[-1]
 		# Create output file
 		outfile = (outdir + filename.split(".")[0] + ".kaks")
-		ck = Popen(split("bin/KaKs_Calculator -i " + axt + " -o " +
-						 outfile + " -m " + method), stdout = DEVNULL)
+		cmd = "bin/KaKs_Calculator -i "+axt+" -o "+outfile+" -m "+method
+		ck = Popen(split(cmd), stdout = DEVNULL)
 		ck.wait()
 	if ck.returncode() == 0:
 		return True
@@ -69,8 +69,8 @@ def main():
 KaKs_Calculator on a directory.")
 	parser.add_argument("-i", help = "Path to input file.")
 	parser.add_argument("-o", help = "Path to output file.")
-	parser.add_argument("-m", help = "Method for calculating Ka/Ks.") 
-	parser.add_argument("-t", type = int, help = "Number of threads.")
+	parser.add_argument("-m", default = "NG", help = "Method for calculating Ka/Ks.") 
+	parser.add_argument("-t", type = int, default = 1, help = "Number of threads.")
 	# Parse arguments and assign to variables
 	args = parser.parse_args()
 	indir = args.i