generateChrDist.py

#################################
######### SiLiCO v. 1.0 #########
### (c)2016 Ethan A. G. Baker ###
##### ethanagbaker@pitt.edu #####
#################################

import numpy as np
import sys, os

#Generates an index file of chromosome lengths. 
def generateChrDist(names):
	#Get the list of chromosome names from splitGenome.py
	with open('SiLiCO_Scratch/chrdist.td','w+') as outfile2:
		for chrom in names:
			#Strip header lines from fasta for processing
			with open("SiLiCO_Scratch/" + str(chrom) + '.fa','r') as infile, open("SiLiCO_Scratch/" + str(chrom) + '.noheader.fa','w+') as outfile:
				for i, line in enumerate(infile):
					if i >= 0:
						if not line.startswith('>'):
							outfile.write(line)
			infile.close()
			outfile.close()  
			#Remove any newline chars, remove undefined nts, make all nts uppercase for processing. 
			with open("SiLiCO_Scratch/" + str(chrom) + '.noheader.fa','r') as infile, \
			open("SiLiCO_Scratch/" + str(chrom) + '.clean.fa','w+') as outfile:
				lines = infile.readlines()
				x = map(str.strip,lines)
				seq = ''
				for line in x:
					y = str(line)
					z = y.upper()
					w = z.replace('N','')
					seq += w
				outfile.write(seq)
				outfile2.write(str(chrom) + '\t' + str(len(seq)) + '\n')
			infile.close()
			outfile.close()
	outfile2.close()

	#Remove all temporary files from the scratch dir
	for chrom in names:
		os.remove("SiLiCO_Scratch/" + str(chrom) + '.noheader.fa')
		os.remove("SiLiCO_Scratch/" + str(chrom) + '.clean.fa')

if __name__ == "__main__":
	generateChrDist(names)