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