def get_ref(chrom, pos, fasta):
'''Read in fasta file'''
def chr_replace(chrom, orig, new): # map PLINK chrom to fasta chrom
chrom_nochr = [re.sub("chr", "", x) for x in chrom]
return [new if x in orig else x for x in chrom_nochr]
complements = {"A": "T", "T": "A", "C": "G", "G": "C"}
fa_ = Fasta(fasta, sequence_always_upper=True,
as_raw=True, read_ahead=900000)
fa_.records = {re.sub("chr", "", x): y for x, y in
zip(fa_.records.keys(), fa_.records.values())}
# steps to keep sex chromosomes and mitochondria by mapping sequences #
mitochroms = ['26', 'M', 'MT', '0M']
if 'M' in fa_.records:
chrom = chr_replace(chrom, mitochroms, 'M')
elif 'MT' in fa_.records:
chrom = chr_replace(chrom, mitochroms, 'MT')
chrom = chr_replace(chrom, ['23', '25', 'XY'], 'X')
chrom = chr_replace(chrom, ['24'], 'Y')
# done mapping sequences #
infa = set(fa_.records.keys()) # chr in fasta file.
cond = [chr_ in infa for chr_ in chrom] # test if chr in fasta
ref = [fa_[x][int(y) - 1] if z else "N"
for x, y, z in zip(chrom, pos, cond)]
comp = [complements.get(x) for x in ref] # get complements of ref allele
fa_.close() # Close fasta file
return ref, comp, infa
