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 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}
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}