def m80_Fasta():
'''
Create a Fasta which doesn't get
returned. Access the Fasta through
the m80 API
'''
# delete the onl
m80tools.delete('Fasta','ACGT',force=True)
f = Fasta.from_file('ACGT','raw/ACGT.fasta')
return True
def print_flank_sequence(vcf,fasta,out,window=30):
vcf = pysam.VariantFile(vcf)
if not available("Fasta",'temp'):
fasta = Fasta.from_file('temp',fasta)
else:
fasta = Fasta('temp')
with open(out,'w') as OUT:
for i,var in enumerate(vcf):
# Grab the FASTA flank sequence
if fasta[var.chrom][var.pos] != var.ref:
print(f"{var.id} REF does not match the FASTA. oops.")
# Grab the probe sequence anyways
kmer = ''.join(fasta[var.chrom][var.pos+1:var.pos+window]).upper()
print(">{}.{}_{}\n{}".format(var.chrom, var.pos, "1", kmer),file=OUT)
kmer = ''.join(fasta[var.chrom][var.pos-window:var.pos-1]).upper()
print(">{}.{}_{}\n{}".format(var.chrom, var.pos, "2", kmer),file=OUT)
def _add_fasta(self, fasta):
'''
Add a reference geneome sequence to the database.
This reference sequence will be used to sort and
conform the genotype (VCF) files used for imputation.
A fasta can only be attached once to a hapdab.
Parameters
----------
fasta : str, path-like or a locuspocus.Fasta object
Path to the fasta file
Returns
-------
None if successful. See the API for accessing the
fasta object.
Raises
------
ValueError if a fasta has already been assigned to the
database.
'''
if 'Fasta' in self._dict:
raise ValueError(
'A Fasta has already been assigned to this database!')
if os.path.exists(fasta):
f = Fasta.from_file(self._m80_name, fasta, parent=self)
elif m80.Tools.available('Fasta', fasta):
f = Fasta(fasta)
os.symlink(f._basedir,
os.path.join(self._basedir, f'Fasta.{f._m80_name}'))
else:
raise ValueError(f'Unable to determine the type of fasta')
self._fasta = f
# and remember for next time
self._dict['Fasta'] = f._m80_name