SAMparser.py

from simplesam import Reader, Writer
import inspect
import sys, os, fileinput, string

in_file = open(sys.argv[1], 'r')
in_sam = Reader(in_file)
out_file = open('full_ecoli_mapped_q10_truth.txt', 'w')
# out_sam = Writer(out_file)

x = next(in_sam)

try:
	while(x.qname != ''):
		#if(x.reverse):
		#	out_file.write("+" + " ")
		#else:
		#	out_file.write("-" + " ")
		out_file.write(x.rname + " ")
		out_file.write(x.qname + " ")
		out_file.write(str(x.pos) + " ")
		out_file.write(str(x.pos + len(x.seq)) + "\n")
		#print str(type(x))
		x = next(in_sam)
except:
	print("Long read alignment ground truth generated")

in_file.close()
out_file.close()