# HG changeset patch
# User izsam
# Date 1426780010 14400
# Node ID 37392af48c377132650d96a27cec4dad148755e3

Uploaded

diff -r 000000000000 -r 37392af48c37 convert.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert.xml	Thu Mar 19 11:46:50 2015 -0400
@@ -0,0 +1,47 @@
+<tool id="phylogeny_converter" name="phylogeny_converter">
+	<description></description>
+	  <command interpreter="python">
+		converter.py $input $output $filetype.inouttype $filetype.type
+	  </command>
+	<inputs>
+        <conditional name="filetype">
+                <param name="type" type="select" label="is this a multi-sequence file?">
+                    <option value="multi">Multi sequence</option>
+                    <option value="single">Single sequence</option>
+                </param>
+                <when value="single">
+	                <param name="input" type="data" label="Original sigle sequence file"/>
+                	<param name="inouttype" type="select" label="conversion">
+                    		<option value="f-g">Fasta to GenBank</option>
+                    		<option value="g-f">GenBank to Fasta</option>
+                	</param>
+                </when>
+                <when value="multi">
+	        	<param name="input" type="data" label="Original multi sequence file" help="Please note that Phylip and nexus limit sequence names to a maximum of 10 characters"/>
+                	<param name="inouttype" type="select" label="conversion">
+                	    <option value="f-g">Fasta to GenBank</option>
+                	    <option value="g-f">GenBank to Fasta</option>
+                	    <option value="f-p">Fasta to Phylip</option>
+                	    <option value="f-n">Fasta to Nexus</option>
+                	    <option value="p-f">Phylip to Fasta</option>
+			    <option value="p-n">Phylip to Nexus</option>
+			    <option value="n-p">Nexus to Phylip</option>
+			    <option value="n-f">Nexus to Fasta</option>
+                	</param>
+                </when>
+        </conditional>
+	</inputs>
+	<outputs>
+		<data name="output" format="tabular"/>
+	</outputs>
+	<help>
+
+What it does
+
+This tool converts different file formats to allow the data-exchange from different philogeny tools.
+
+Developed by 
+Iolanda Mangone
+
+	</help>
+</tool>
diff -r 000000000000 -r 37392af48c37 converter.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/converter.py	Thu Mar 19 11:46:50 2015 -0400
@@ -0,0 +1,535 @@
+
+#!/usr/bin/env python
+
+import sys
+import string
+import os
+
+class convertitori:
+	def __init__(self,input,inouttype,type,output):
+		self.input = input
+		self.inouttype = inouttype
+		self.type = type
+		self.output = output
+
+	def fp(self):
+		count = 0
+		cseq = 0
+		fasta = []
+		for riga in self.input:
+			count += 1
+		        if ">" in riga:
+		                f = ""
+		                p = self.input.index(riga,count-1)
+		                c = 1
+                                y = riga[1:].replace(" ","_")
+                                if y >= 10:
+                                        f = f + y[:10] + '\t'
+                                else:
+                                        f = f + y + "_"*(10-len(y)) + '\t'
+				try:
+			                while ">" not in self.input[p+c]:
+			                        f = f + (self.input[p+c].strip())
+			                        c += 1
+				except:
+					pass
+				fasta.append(f)
+		num = str(len(fasta))
+		lun = str(len(fasta[0].split("\t")[1]))
+		for sequence in fasta:
+			if str(len(sequence.split("\t")[1])) != lun:
+				sys.exit("The input file does not contains a multiple alignment in fasta format. Please ensure that all the sequences have the same length")
+		self.output.write(num + '\t' + lun + '\n')
+		for seq in fasta:
+		        self.output.write(seq + '\n')
+
+	def fn(self):
+		count = 0
+		fasta = []
+		for riga in self.input:
+			count += 1
+		        if ">" in riga:
+		                f = ""
+		                p = self.input.index(riga,count-1)
+		                c = 1
+				y = riga[1:].replace(" ","_")
+				if y >= 10:
+			                f = f + y[:10] + '\t'
+				else:
+					f = f + y + "_"*(10-len(y)) + '\t'
+				try:
+                                        while ">" not in self.input[p+c]:
+                                                f = f + (self.input[p+c].strip())
+                                                c += 1
+				except:
+					pass
+				fasta.append(f)
+		num = str(len(fasta))
+		lun = str(len(fasta[0].split("\t")[1]))
+		for sequence in fasta:
+			if str(len(sequence.split("\t")[1])) != lun:
+				sys.exit("The input file does not contains a multiple alignment in fasta format. Please ensure that all the sequences have the same length")
+		self.output.write("#NEXUS\n\nBEGIN DATA;\nDIMENSIONS NTAX=%s NCHAR=%s;\nFORMAT DATATYPE=DNA INTERLEAVE MISSING=-;\n\nMATRIX\n"%(num,lun))
+		porzioni = int(lun)/100
+		for volte in range(porzioni):
+			for seq in fasta:
+				part = ""
+				self.output.write(seq.split("\t")[0] + '\t')
+				cont = 0
+				for chara in seq.split("\t")[1][volte*100:(volte+1)*100]:
+					cont += 1
+					part = part + chara
+					if cont%20.0 == 0:
+						part = part + " "
+				part = part + "\n"
+				self.output.write(part)
+			self.output.write("\n\n\n")
+		for seq in fasta:
+			part = ""
+			cont = 0
+			self.output.write(seq.split("\t")[0] + '\t')
+			for chara in seq.split("\t")[1][(volte+1)*100:]:
+				cont += 1
+				part = part + chara
+				if cont%20.0 == 0:
+					part = part + " "
+			part = part + "\n"
+			self.output.write(part)
+
+	def pn(self):
+		num = int(self.input[0].split()[0])
+		lun = float(self.input[0].split()[1])
+		lunf = float(len(self.input))
+		self.output.write("#NEXUS\n\nBEGIN DATA;\nDIMENSIONS NTAX=%s NCHAR=%s;\nFORMAT DATATYPE=DNA INTERLEAVE MISSING=-;\n\nMATRIX\n"%(int(num),lun))
+		spia = 0
+		porzioni = int(lun)/100
+		if (lunf-1)/num == 1.0:
+			spia = 1
+		if spia == 1:
+			for volte in range(porzioni):
+				for seq in self.input[1:]:
+	                                part = ""
+	                                self.output.write(seq.split("\t")[0] + '\t')
+	                                cont = 0
+	                                for chara in seq.split("\t")[1][volte*100:(volte+1)*100]:
+	                                        cont += 1
+	                                        part = part + chara
+	                                        if cont%20.0 == 0:
+	                                                part = part + " "
+	                                part = part + "\n"
+	                                self.output.write(part)
+	                        self.output.write("\n\n\n")
+                	for seq in self.input[1:]:
+	                        part = ""
+	                        cont = 0
+	                        self.output.write(seq.split("\t")[0] + '\t')
+	                        for chara in seq.split("\t")[1][(volte+1)*100:]:
+	                                cont += 1
+	                                part = part + chara
+	                                if cont%20.0 == 0:
+	                                        part = part + " "
+	                        part = part + "\n"
+	                        self.output.write(part)
+		else:
+			if len(self.input[1])<=11:
+				for volte in range(porzioni):
+					interm = 0 
+					for seq in self.input[1:]:
+	                                        if seq == "\n":
+	                                                interm += 1
+						if (self.input.index(seq)+interm)%2 == 0 and seq != "\n":
+			                                part = ""
+			                                cont = 0
+			                                for chara in seq[volte*100:(volte+1)*100]:
+			                                        cont += 1
+			                                        part = part + chara
+			                                        if cont%20.0 == 0:
+			                                                part = part + " "
+			                                part = part + "\n"
+			                                self.output.write(part)
+	                                        elif (self.input.index(seq)+interm)%2 != 0 and seq != "\n":
+        	                                        self.output.write(seq[:10] + "\t")
+					self.output.write("\n\n\n")
+				interm = 0
+		                for seq in self.input[1:]:
+	                        	if seq == "\n":
+	                                        interm += 1
+					if (self.input.index(seq)+interm)%2 == 0 and seq != "\n":
+				                part = ""
+				                cont = 0
+				                for chara in seq[(volte+1)*100:]:
+				 	                cont += 1
+				                        part = part + chara
+				                        if cont%20.0 == 0:
+			        	                	part = part + " "
+			                	part = part + "\n"
+			                        self.output.write(part)
+					elif (self.input.index(seq)+interm)%2 != 0 and seq != "\n":
+        	                                self.output.write(seq[:10] + "\t")
+			else:
+				try:
+					diz = {}
+					volta = 0
+					for riga in self.input[1:]:
+						if self.input.index(riga) in range(num+1):
+							numriga = self.input.index(riga)
+							diz[self.input.index(riga)] = [self.input[numriga][:10],self.input[numriga][10:].strip().replace(" ","")]
+						else:
+							if riga == "\n":
+								volta += 1
+							else:
+								numriga = self.input.index(riga)
+								prima = diz[numriga - ((num+1)*volta)][1] + self.input[self.input.index(riga)].strip().replace(" ","")
+								diz[numriga - ((num+1)*volta)] = [diz[numriga - ((num+1)*volta)][0],prima]
+	                                for volte in range(porzioni):
+	                                        for seq in diz.keys():
+	                                        	cont = 0
+							self.output.write(diz[seq][0] + "\t")
+							for chara in diz[seq][1][volte*100:(volte+1)*100]:
+		                                                self.output.write(chara)
+	                                                        cont += 1
+                                                                if cont%20.0 == 0:
+                                                                        self.output.write(" ")
+	                                                self.output.write("\n")
+	                                        self.output.write("\n\n\n")
+                                        for seq in diz.keys():
+                                                cont = 0
+                                                self.output.write(diz[seq][0] + "\t")
+                                                for chara in diz[seq][1][(volte+1)*100:]:
+	                                                self.output.write(chara)
+                                                        cont += 1
+                                                        if cont%20.0 == 0:
+                                                                self.output.write(" ")
+                                                self.output.write("\n")
+				except:
+					sys.exit("The input file is not in the proper format. Please check that your file is in Phylip standard interleaved (or sequential) format ")
+					
+	def pf(self):
+		num = int(self.input[0].split()[0])
+		lun = float(len(self.input))
+		spia = 0
+		if (lun-1)/num == 1.0:
+			spia = 1
+		if spia == 1:
+			for riga in self.input[1:]:
+				for ele in range(int(lun-1)):
+					cont = 0
+					self.output.write(">" + self.input[ele+1][:10] + "\n")
+					for char in self.input[ele+1][10:].strip().replace(" ",""):
+						self.output.write(char)
+						cont += 1
+						if cont%80.0 == 0:
+							self.output.write('\n')
+					self.output.write('\n')
+		else:
+			if len(self.input[1])<=11:
+				interm = 0
+				for riga in self.input[1:]:
+					if riga == "\n":
+						interm += 1
+					if (self.input.index(riga)+interm)%2 == 0 and riga != "\n":
+						cont = 0
+						for char in riga.strip().replace(" ",""):
+	                                	        self.output.write(char)
+	                                                cont += 1
+	                                                if cont%80.0 == 0:
+	                                        	        self.output.write('\n')
+	                                        self.output.write('\n')
+					elif (self.input.index(riga)+interm)%2 != 0 and riga != "\n":
+	                                        self.output.write(">" + riga[:10] + "\n")
+			else:
+				try:
+					diz = {}
+					volta = 0
+					for riga in self.input[1:]:
+						if self.input.index(riga) in range(num+1):
+							numriga = self.input.index(riga)
+							diz[self.input.index(riga)] = [self.input[numriga][:10],self.input[numriga][10:].strip().replace(" ","")]
+						else:
+							if riga == "\n":
+								volta += 1
+							else:
+								numriga = self.input.index(riga)
+								prima = diz[numriga - ((num+1)*volta)][1] + self.input[self.input.index(riga)].strip().replace(" ","")
+								diz[numriga - ((num+1)*volta)] = [diz[numriga - ((num+1)*volta)][0],prima]
+					for elemento in diz.keys():
+						self.output.write(">" + diz[elemento][0] + '\n')
+						con = 0
+						for char in diz[elemento][1]:
+							self.output.write(char)
+							con += 1
+							if con%80 == 0:
+								self.output.write('\n')
+						self.output.write('\n')
+				except:
+					sys.exit("The input file is not in the proper format. Please check that your file is in Phylip standard interleaved (or sequential) format ")
+
+	def nf(self):
+		try:
+			diz = {}
+			spia = 0
+			for riga in self.input:
+				if "MATRIX" in riga:
+					spia = 1
+				if spia == 1 and "MATRIX" not in riga and riga != "\n":
+					if riga.split()[0] not in diz.keys():
+						diz[riga.split()[0]] = ""
+					else:
+						for ele in riga.split()[1:]:
+							diz[riga.split()[0]] = diz[riga.split()[0]] + ele.strip()
+			for elemento in diz.keys():
+				self.output.write(">" + elemento + '\n')
+				con = 0
+				for char in diz[elemento]:
+					self.output.write(char)
+					con += 1
+					if con%80 == 0:
+						self.output.write('\n')
+				self.output.write('\n')
+		except:
+			sys.exit("The input file is not in Nexus format. ")
+
+	def np(self):
+		try:
+			diz = {}
+			spia = 0
+			for riga in self.input:
+				if "MATRIX" in riga:
+					spia = 1
+				if spia == 1 and "MATRIX" not in riga and riga != "\n":
+					if riga.split()[0] not in diz.keys():
+						diz[riga.split()[0]] = ""
+					else:
+						for ele in riga.split()[1:]:
+							diz[riga.split()[0]] = diz[riga.split()[0]] + ele.strip()
+	                num = str(len(diz.keys()))
+	                lun = str(len(diz.values()[0]))
+	                self.output.write(num + '\t' + lun + '\n')
+			for elemento in diz.keys():
+	                        if elemento >= 10:
+	                        	nome = elemento[:10] + '\t'
+	                        else:
+	                                nome = elemento + "_"*(10-len(elemento)) + '\t'
+	                        self.output.write(nome + diz[elemento] + '\n')
+		except:
+			sys.exit("The input file is not in Nexus format. ")
+
+					
+	def fg(self):
+		count = 0
+		fasta = []
+		for riga in self.input:
+			count += 1
+		        if ">" in riga:
+		                f = ""
+		                p = self.input.index(riga,count-1)
+		                c = 1
+				y = riga[1:-1].replace(" ","_")
+			        f = f + y + '\t'
+				try:
+                                        while ">" not in self.input[p+c]:
+                                                f = f + (self.input[p+c].strip())
+                                                c += 1
+				except:
+					pass
+				fasta.append(f)
+		for seq in fasta:
+			lun = str(len(seq.split("\t")[1]))
+			self.output.write("LOCUS\t%s\t%s bp\nORIGIN\n"%(seq.split("\t")[0],lun))
+			porzioni = int(lun)/60
+			cont = 0
+			for volte in range(porzioni):
+				part = ""
+				self.output.write(str(cont+1) + "\t")
+				for chara in seq.split("\t")[1][volte*60:(volte+1)*60]:
+					cont += 1
+					part = part + chara
+					if cont%10.0 == 0:
+						part = part + " "
+				self.output.write(part)
+                        	self.output.write("\n")
+			self.output.write(str(cont+1) + "\t")
+			part = ""
+			for chara in seq.split("\t")[1][(volte+1)*60:]:
+				cont += 1
+				part = part + chara
+				if cont%10.0 == 0:
+					part = part + " "
+			self.output.write(part)
+			self.output.write("\n")
+			self.output.write("//\n\n")
+
+	def gf(self):
+		for riga in self.input:
+			if "LOCUS" in riga:
+				nome = ""
+				spia = 0
+				len = ""
+				seq = ""
+				part = riga.split()
+				for ele in part:
+					if "bp" in ele:
+						len = str(riga.index(ele)-1)
+				nome = part[1] + '\t'
+			if "DEFINITION" in riga:
+				part = riga.split()
+				for ele in part[1:]:
+					nome = nome + ele + ' ' 
+			if "ORIGIN" in riga:
+				spia = 1
+			if spia == 1 and "ORIGIN" not in riga:
+				part = riga.split()
+				for ele in part[1:]:
+					seq = seq + ele.strip()
+			if "//" in riga:
+				self.output.write(">" + nome + '\n')
+				con = 0
+				for char in seq:
+					self.output.write(char)
+					con += 1
+					if con%80 == 0:
+						self.output.write('\n')
+				self.output.write('\n')
+				spia = 0
+
+class check_fileformat:
+        def __init__(self,inouttype,input):
+                self.intype = inouttype[0]
+		self.infile = input
+	def single(self):
+		if self.intype == "f":
+			count = 0
+			for riga in self.infile:
+				if riga[0] == ">":
+					count += 1
+			if count == 1:
+				if len(self.infile) < 2:
+					sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
+				else:
+					return "ok"
+			else:
+				if count >1:
+					sys.exit("The input file is a multi-fasta file. Please resubmit the job using the 'multi sequence' option")
+				if count == 0:
+					sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
+		if self.intype == "g":
+			locus = 0
+			origin = 0
+			end = 0
+			lun = 1
+			for riga in self.infile:
+				if "LOCUS" in riga:
+					locus = 1
+				if "ORIGIN" in riga:
+					origin = 1
+				elif origin == 1 and len(riga.split()) >= 7:
+					lun = 0
+				if "//" in riga:
+					end = 1
+			if locus == 0 or origin == 0 or end == 0 or lun == 1:
+				sys.exit("The input file is not in GenBank format. Please make sure that the file contains at least the LOCUS and ORIGIN fields. The file must also ends with //")
+			else:
+				return "ok" 
+	def multi(self):
+		if self.intype == "p":
+			if len(self.infile[0].split()) == 2 or len(self.infile[0].split()) == 3:
+				if int(self.infile[0].split()[0]) > 1:
+					return "ok"
+				else:
+					sys.exit("There is only one sequence in the file")
+			else:
+				sys.exit("the input file is not in phylip format.")
+		if self.intype == "n":
+			begin = 0
+			matrix = 0
+			ntax = 0
+			if "#NEXUS" in self.infile[0]:
+				for riga in self.infile:
+					if "begin data;" in riga.lower():
+						begin = 1
+					if "matrix" in riga.lower():
+						matrix = 1
+					if "ntax" in riga.lower():
+						r = riga.split()
+						ntax = int(r[1][5:])
+				if begin==1 and matrix == 1:
+					return "ok"
+				else:
+					sys.exit("the input file is not in nexus format.")
+				if ntax <= 1:
+					 sys.exit("There is only one sequence in the file")				
+			else:
+				sys.exit("the input file is not in nexus format.")
+		if self.intype == "f":
+			count = 0
+			for riga in self.infile:
+				if riga[0] == ">":
+					count += 1
+			if count > 1:
+				if len(self.infile) < 4:
+					sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
+				else:
+					return "ok"
+			else:
+				if count == 1:
+					sys.exit("The input file is a single-fasta file. Please resubmit the job using the 'single sequence' option")
+				if count == 0:
+					sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
+		if self.intype == "g":
+			locus = 0
+			origin = 0
+			end = 0
+			lun = 1
+			for riga in self.infile:
+				if "LOCUS" in riga:
+					locus = 1
+				if "ORIGIN" in riga:
+					origin = 1
+				if origin == 1 and len(riga.split()) >= 7:
+					lun = 0
+				if "//" in riga:
+					end = 1
+			if locus == 0 or origin == 0 or end == 0 or lun == 1:
+				sys.exit("The input file is not in GenBank format. Please make sure that the file contains at least the LOCUS and ORIGIN fields. The file must also ends with //")
+			else:
+				return "ok"
+
+
+def main(input,output,inouttype,type):
+	check = check_fileformat(inouttype,input)
+	if type == "single":
+		c = check.single()
+		if c == "ok":
+			conv = convertitori(input,inouttype,type,output)
+	                if inouttype == "f-g":
+	                        conv.fg()
+	                if inouttype == "g-f":
+	                        conv.gf()
+	if type == "multi":
+		c = check.multi()
+		if c == "ok":
+			conv = convertitori(input,inouttype,type,output)
+			if inouttype == "f-g":
+				conv.fg()
+			if inouttype == "g-f":
+				conv.gf()
+			if inouttype == "f-p":
+				conv.fp()
+			if inouttype == "f-n":
+				conv.fn()
+			if inouttype == "p-f":
+				conv.pf()
+			if inouttype == "p-n":
+				conv.pn()
+			if inouttype == "n-p":
+				conv.np()
+			if inouttype == "n-f":
+				conv.nf()
+	output.close()
+
+if __name__ == "__main__" : 
+	input = open(sys.argv[1],"r").readlines()
+	output = open(sys.argv[2],"a")
+	inouttype = sys.argv[3]
+        type = sys.argv[4]
+	main(input,output,inouttype,type)