annotate 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

#!/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)