Return the sequence from a FASTA file given a start and end position

getRef.py

#License: CC0 Public Domain (2017) Ahmad Retha

##
# Get range of bases from a fasta file. e.g. chr21:9411239-9411240
# @param refFile The fasta filename e.g. Homo_sapiens.GRCh37.75.dna.chromosome.21.fa
# @param begin 1-based index in sequence e.g. 9411239
# @param end 1-based index in sequence up-to-but-not-including e.g. 9411240
# @return string 'G'
def getRef(refFile, begin, end):
	if begin > end:
		begin, end = end, begin
	elif begin == end or begin < 1 or end < 1:
		return ''
	seq = ''
	with open(refFile, 'r') as rf:
		j = 1
		for line in rf:
			line = line.strip()
			if line == '' or line.startswith('>'):
				continue
			if j >= end:
				break
			lineLen = len(line)
			if j+lineLen >= begin:
				k = 0
				while j+k < begin:
					k += 1
				j = j + k
				while j < end and k < lineLen:
					seq += line[k]
					j += 1
					k += 1
			else:
				j += lineLen
	return seq

print getRef('./Homo_sapiens.GRCh37.75.dna.chromosome.21.fa', 9411239, 9411240)