diff bin/design_matrix_creator @ 1:a4a4c88783ea draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/design_matrix_creator	Tue Sep 01 04:59:05 2015 -0400
@@ -0,0 +1,222 @@
+#!/usr/bin/env python
+
+import argparse, os, shutil, sys, tempfile, subprocess
+
+__version_info__ = ('1', '0', '0')#, 'beta')
+__version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3])+"-"+__version_info__[3]
+__author__ = 'Youri Hoogstrate'
+__homepage__ = 'https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools'
+__license__ = 'GNU General Public License v3 (GPLv3)'
+
+
+class sampleContainer:
+	def __init__(self):
+		self.samples = []
+		self.treatments = {}
+		self.treatment_index = []
+		self.treatment_types = {}
+	
+	def do_decode(self,encoded_str):
+		return encoded_str.decode("base64").strip().replace("\t",'')
+	
+	def add_samples(self,argument):
+		print " - Adding samples"
+		for sample in argument:
+			self.add_sample(self.do_decode(sample))
+	
+	def add_sample(self,sample):
+		if(sample in self.samples):
+			sys.stderr.write("Error:\n* Non-unique sample: "+sample+"\n")
+			sys.exit(1)
+		else:
+			self.samples.append(sample)
+			print "     - Added: "+sample
+	
+	def add_blocking(self,argument):
+		print " - Adding paired samples"
+		pair = []
+		for block in argument:
+			self.add_block(block)
+	
+	def add_block(self,blocks):
+		blocks = blocks.split(":")
+		as_treatment = blocks[0]
+		blocks = blocks[1:]
+		
+		used_samples = []
+		indexed_samples = {}
+		
+		for i in range(len(blocks)):
+			block = blocks[i]
+			samples = self.get_samples_from_block(block)
+			indexed_samples[i+1] = []
+			for sample in samples:
+				if(sample in used_samples):
+					sys.stderr.write("Error:\n* Blocking contains multiple times the same sample: "+sample+"\n")
+					sys.exit(0)
+				else:
+					indexed_samples[i+1] = block
+				used_samples.append(sample)
+		
+		for sample in self.samples:
+			if(sample not in used_samples):
+				i = i + 1
+				indexed_samples[i+1] = str(sample).encode('base64').strip()
+		
+		for index in indexed_samples.keys():
+			key = str(index).encode('base64').strip()
+			as_treatment += ":"+key+":"+indexed_samples[index]
+		
+		self.add_treatment(as_treatment)
+	
+	def get_samples_from_block(self,decoded_block):
+		return [ self.do_decode(x) for x in decoded_block.split(",")]
+	
+	def add_treatments(self,argument):
+		print " - Adding treatments"
+		for treatment in argument:
+			self.add_treatment(treatment)
+	
+	def add_treatment(self,treatment_argument):
+		print " - Parsing treatment"
+		
+		
+		treatment_argument = treatment_argument.split(":")
+		name = self.do_decode(treatment_argument[0])
+		treatment_argument = treatment_argument[1:]
+		
+		
+		treatment = {"factor_index":{},"sample_index":{}}
+		only_integers = True
+		
+		i = 1
+		for item in treatment_argument:
+			if(i % 2):
+				factor = self.do_decode(item)
+				
+				if(treatment['factor_index'].has_key(factor)):
+					sys.stderr.write("Error:\n* Factor has been added multiple times to treatment: "+factor+"\n")
+					sys.exit(0)
+				else:
+					print "   - Adding factor: "+factor
+					treatment["factor_index"][factor] = []
+					if(not factor.isdigit()):
+						only_integers = False
+			else:
+				for sample in item.split(","):
+					sample = self.do_decode(sample)
+					
+					if(not sample in self.samples):
+						sys.stderr.write("Error:\n* Unknown sample: "+sample+"\n")
+						sys.exit(0)
+					
+					treatment["factor_index"][factor].append(sample)
+					if(treatment["sample_index"].has_key(sample)):
+						sys.stderr.write("Error:\n* Factor has been added to treatment before: "+sample+"/"+factor+", factors must be mutually exclusive!\n")
+						sys.exit(0)
+					else:
+						treatment["sample_index"][sample] = factor
+			i += 1
+		
+		treatment_factors = sorted(treatment["factor_index"].keys())
+		
+		if(name == None):
+			treatment["name"] = "_vs_".join(treatment_factors)
+		else:
+			treatment["name"] = str(name)
+		
+		if(len(treatment["sample_index"]) != len(self.samples)):
+			sys.stderr.write("Error:\n* The number of samples for treatment '"+treatment["name"]+"' ("+str(len(treatment["sample_index"]))+") is different from the total number of samples ("+str(len(self.samples))+").\n")
+		
+		if(only_integers):
+			treatment_type = "integer"
+		else:
+			treatment_type = "string"
+		
+		if(self.treatments.has_key(treatment["name"])):
+			sys.stderr.write("Error:\n* Treatment was already added: '"+treatment["name"]+"\n")
+		else:
+			self.treatments[treatment["name"]] = treatment
+			self.treatment_index.append(treatment["name"])
+			self.treatment_types[treatment["name"]] = treatment_type
+			print "     - Treatment \""+treatment["name"]+"\" of type \""+treatment_type+"\" is valid"
+	
+	def export(self,output):
+		# Open file stream
+		if(args.output == "-"):
+			fh = sys.stdout
+		else:
+			fh = open(args.output,"w")
+		
+		# Write header:
+		fh.write("sample-name\t"+"\t".join(self.treatment_index)+"\n")
+		
+		# Write body:
+		for sample in self.samples:
+			fh.write(sample)
+			for treatment_id in self.treatment_index:
+				treatment = self.treatments[treatment_id]
+				fh.write("\t"+treatment["sample_index"][sample])
+			fh.write("\n")
+		
+		fh.close()
+
+if __name__=="__main__":
+	parser = argparse.ArgumentParser(description="Create an edgeR design matrix with read-count datasets.")
+	parser.add_argument("-o","--output", help="Output file, '-' for stdout.",required=True)
+	parser.add_argument("-c","--columns-file", nargs="?", help='Use columns of [this] file as UIDs (counting from 1)')
+	parser.add_argument("-s","--sample-names", nargs="*", help='Sample names (UIDs that correspond to the columns in the expression matrix)')
+	parser.add_argument("-t","--treatments", nargs="+", help='Treatment or conditions: "name::sample:condition& (sample-names and conditions have to be provided using Base64 encoding to avoid weird characters)',required=True)
+	parser.add_argument("-b","--blocking", nargs="+", help='Description of sample blocking: "blocking_condition*&sample-1-name&sample-2-name&sample-n-name"')
+	
+	args = parser.parse_args()
+	
+	columns = None
+	if(args.columns_file):
+		with open(args.columns_file, "r") as f:
+			listed_columns = [None] + f.readline().strip("\n").split("\t")
+			for i in range(1,len(listed_columns)):
+				listed_columns[i] =  listed_columns[i].encode('base64').replace('\n','')
+	
+	s = sampleContainer()
+	
+	if(listed_columns):
+		columns = []
+		for sample in args.sample_names:
+			columns.append(listed_columns[int(sample)])
+		
+		
+		treatments = []
+		for treatment in args.treatments:
+			treatment = treatment.split(":")
+			for i in range(1,len(treatment)):
+				if(i%2 == 0):
+					treatment_tmp = treatment[i].split(",")
+					for j in range(len(treatment_tmp)):
+						treatment_tmp[j] = listed_columns[int(treatment_tmp[j])]
+					treatment[i] = ",".join(treatment_tmp)
+					
+			treatments.append(":".join(treatment))
+		
+		blockings = []
+		if(args.blocking):
+			for blocking in args.blocking:
+				blocking = blocking.split(":")
+				for i in range(1,len(blocking)):
+					block = blocking[i].split(",")
+					for j in range(len(block)):
+						block[j] = listed_columns[int(block[j])]
+					blocking[i] = ",".join(block)
+				blockings.append(":".join(blocking))
+		
+		s.add_samples(columns)
+		s.add_treatments(treatments)
+		s.add_blocking(blockings)
+	
+	else:
+		s.add_samples(args.sample_names)
+		s.add_treatments(args.treatments)
+		if(args.blocking):
+			s.add_blocking(args.blocking)
+	
+	s.export(args.output)