Compile_annotation_files.py

"""
Compile annotation files


"""
import os, sys, gzip, datetime


def main():

	input_file_counts = open("/gpfs/group/stsi/data/projects/wellderly/GenomeComb/annotations/table2.counter.final")
	input_file_novel = open("/gpfs/group/stsi/data/projects/wellderly/GenomeComb/annotations/table2.counter.thousandG")

	outfile_file_cunts = open("/gpfs/group/stsi/data/projects/wellderly/GenomeComb/annotations/table2.counter.compiled", "w")
	outfile_file_novel = open("/gpfs/group/stsi/data/projects/wellderly/GenomeComb/annotations/table2.counter.thousandg.compiled", "w")
	
	count_dict = {}
	novel_dict = {}
	for line in input_file_counts:
		tp_line = line.strip().split("\t")
		dict_key = tp_line[1]
		val_array = tp_line[2:]
		#see if this entry was already found
		try:
			val = count_dict[dict_key]
			new_val = []
			#add the new stuff
			for index, i in val:
				new_val_t = int(val_array[index])+int(i)
				new_val.append(new_val_t)

			#add new data to the dictionary
			count_dict[dict_key] = new_val
		except:
			count_dict[dict_key] = val_array

	input_file_counts.close()

	for i in count_dict:
		counts = count_dict[i]
		outfile_file_cunts.write(i+ "\t" + str(counts[0])+"\t"+str(counts[1])+"\t"+str(counts[2])+"\n")
	outfile_file_cunts.close()

	#Compile the novel data
	for line in input_file_novel:
		tp_line = line.strip().split("\t")
		dict_key = tp_line[1]
		val_array = tp_line[2:]
		#see if this entry was already found
		try:
			val = novel_dict[dict_key]
			new_val = []
			#add the new stuff
			for index, i in val:
				new_val_t = float(val_array[index])+float(i)
				new_val.append(new_val_t)

			#add new data to the dictionary
			novel_dict[dict_key] = new_val
		except:
			novel_dict[dict_key] = val_array

	input_file_novel.close()

	for i in novel_dict:
		counts = novel_dict[i]
		new_counts = []
		#Since we added the percentage by chromosome, we need to split by 22
		for c in counts:
			n_c = float(c)/22.0
			new_counts.append(n_c)

		outfile_file_novel.write(i+ "\t" + str(new_counts[0])+"\t"+str(new_counts[1])+"\t"+str(new_counts[2])+"\n")
	outfile_file_novel.close()




if __name__ == '__main__':

    print "Python Version: " + sys.version

    import time
    start = time.time()
    main()
    #main(sys.argv[1], sys.argv[2], sys.argv[3])
    end = time.time()
    #print 'This took {0} seconds'.format(end - start)