outMaskedFastaDir='/cellar/users/btsui/Data/ensembl/snp_masked/'
specie='Mus_musculus'
outMaskedFDir=outMaskedFastaDir+specie+'.fa'
testChrom='MT'
startI=152185369
from Bio import SeqIO
import gzip
maskedFasta=outMaskedFDir+'.gz'
#unmaskedFasta='/cellar/users/btsui/Data/ensembl/release/fasta/Homo_sapiens.GRCh38.dna_rm.toplevel.fa'
with gzip.open(maskedFasta, "rb") as handle:
for record in SeqIO.parse(handle=handle, format="fasta") :
print(record.id)
if record.id==testChrom:
break
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y MT
#record[]
#152184370 152186370
#str((record[11546:13546]).seq)