def blastlinkconnector(self, q_seq_fn, s_seq_fn):
# Make files out of seqs
with NamedTemporaryFile(delete=False) as blastout_fh:
blastout_fn = blastout_fh.name
blastn_cli = blastCL(cmd=self.blastn_path,
query=q_seq_fn,
subject=s_seq_fn,
task="blastn-short",
evalue=.00005,
outfmt=5, #m 7
out=blastout_fn)
stdout, stderr = blastn_cli()
return blastout_fn
def blastregular(self, q_seq_fn, db):
# Make files out of seqs
with NamedTemporaryFile(delete=False) as blastout_fh:
blastout_fn = blastout_fh.name
blastn_cli = blastCL(cmd=self.blastn_path,
query=q_seq_fn,
db=db,
word_size=11,
reward=1,
penalty=-5, #-q
gapopen=3, #G
gapextend=3, #E
#dust = "m", #F FIXME
#task='blastn',
evalue=700, #e o 700?
searchsp=1750000000000,
outfmt=5, #m 7
out=blastout_fn) #o
stdout, stderr = blastn_cli()
return blastout_fn
