comparison design_matrix_creator.py @ 52:7fc17dc83777 draft

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51:ca24a51fa144

class sampleContainer:
	def __init__(self):
		self.samples = []
		self.treatments = {}
		self.treatment_types = {}
	
	def do_decode(self,encoded_str):
		return encoded_str.decode("base64").strip().replace("\t",'')
	

		
		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_types[treatment["name"]] = treatment_type
			print "     - Treatment \""+treatment["name"]+"\" of type \""+treatment_type+"\" is valid"
	
	def export(self,output):
		# Open file stream

			fh = sys.stdout
		else:
			fh = open(args.output,"w")
		
		# Write header:
		fh.write("sample-name\t"+"\t".join(self.treatments.keys())+"\n")
		
		# Write body:
		for sample in self.samples:
			fh.write(sample)
			for treatment in self.treatments.keys():
				fh.write("\t"+self.treatments[treatment]["sample_index"][sample])
			fh.write("\n")
		
		fh.close()

if __name__=="__main__":

52:7fc17dc83777

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",'')
	

		
		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

			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__":