def test_read_sequences_from_fasta_string(self): """test reading sequences from a string in FASTA format""" with open("testdata/fasta_test.fa") as inputfile: fasta_string = inputfile.read() seqs = st.read_sequences_from_fasta_string(fasta_string) self.assertEquals(7, len(seqs)) seq = ("CCGAGGAAGACAGACGCAATTTCACATCGAACTCGTGTACGGCATCCTCT" + "TTATTGCCGGCTTTGCTTTTCTCGTCTTCCGCGTCGATCCCCGGGTGGCA" + "GCGTTCGAAGGAGGTCTCGTCATTGGTTACTTATTGAGAATTTAGGGGAA" + "AATGTCAATCTACGAGTGGA") self.assertEquals('VNG6198H', seqs[6][0]) self.assertEquals(seq, seqs[6][1])
def process_with_dust(seqs): """data conversion from and to dust tool""" dust_tmp_file = None with tempfile.NamedTemporaryFile(mode='w+', prefix='dust', delete=False) as dust_input: for feature_id, seq in seqs.items(): dust_input.write(">%s\n" % feature_id) if isinstance(seq, str): dust_input.write("%s\n" % seq) else: dust_input.write("%s\n" % seq) dust_tmp_file = dust_input.name #logging.info("DUST input written to: %s", dust_input.name) seqpairs = st.read_sequences_from_fasta_string( self.dust(dust_tmp_file)) os.remove(dust_tmp_file) return {feature_id: seq for feature_id, seq in seqpairs}