def split_data(fastaFN, partitions):
buckets = [[] for _ in xrange(partitions)]
ring = cycle(xrange(partitions))
with open(fastaFN, 'rU') as inF:
for seq in util.parseFASTA(inF):
buckets[ring.next()].append(seq)
return buckets
def split_data(fastaFN, partitions):
buckets = [[] for _ in xrange(partitions)]
ring = cycle(xrange(partitions))
with open(fastaFN, 'rU') as inF:
for seq in util.parseFASTA(inF):
buckets[ring.next()].append(seq)
return buckets
def test_parseFASTA(self):
"""
Testing parseFASTA function.
:return: Returns OK is test goals were achieved, otherwise raises
error.
"""
FASTARecord = namedtuple("FASTA_Record", "id descr data")
parseFASTA_result = ut.parseFASTA("phylotoast/test/test_FASTA.fna")
manually_parsed = [
FASTARecord(
id="PIDF154_1",
descr=
"HU82XDC01DBOHO orig_bc=ACAGGTCG new_bc=ACAGGTCG bc_diffs=0",
data=
"AGTGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGGAGATTAAGTAGCTTGCTATTTAATCTTAGTGGCGCACGGGTGAGTAATATATAGCTAATCTGCCCTACACTAGAGGACAACAGTTGGAAACGACTGCTAATACTCTATACTCCTTCTTTACATAAGTTAAGTCGGGAAAGTTTTTCGGTGTAGGATGAGGCTATATCGTATCAGCTAGTGGTAGGTAACGGCCTACCAAGGCTATGACGCGTAACTGGTCTGAGAGGATGATCAGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGGAATATTGCTCAAATGGGGGGAAAACCCTGAAAGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGA"
),
FASTARecord(
id="PIDTA158_2",
descr=
"HU82XDC01A3N0T orig_bc=ACCGCAGG new_bc=ACCGCAGG bc_diffs=0",
data=
"GATGAACGCTAGCGATAGGCTTAACACATGCAAGTCGAGGGCATCACGAATTAGCAATAGTTTGGTGGCGACCGGCGCACGGGTGCGTAACACGTATACAACCTACCTTCAATTGGGGAATAACCTGGAGAAATTTGGACTAATACCCCATAGTAAACGGGAGAGGCATTCTTTTTTGTTTAAAGATTTATTGATTGGAGATGGGTATGCGTAGGATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATCCTTAGGGGTT"
),
FASTARecord(
id="PIDF160_3",
descr=
"HU82XDC01DTNIU orig_bc=ACCGTAGA new_bc=ACCGTAGA bc_diffs=0",
data=
"GATGAACGCTGACAGAATGCTTAACACATGCAAGTCTACTTGAACTTCGGTTTGGGTGGCGGACGGGTGAGTAACGCGTAAAGAACTTGCCTCACAGTTAGGGACAACATTTGGAAACGAATGCTAATACCTGATATTATGATTTTAGGGCATCCTAAGATTATGAAAGCTATATGCGCTGTGAGAGAGCTTTGCGTCCCATTAGCTAGTTGGAGAGGTAACGGCTCACCAAGGCGATGATGGGTAGCCGGCCTGAGAGGGTGAACGGGCCACAAGGGGACTGAGACACGGCCCTTACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGACAATGGAACCAAAAGTCTGATCCAGCAATTCTGTGTGCACGATG"
),
FASTARecord(
id="PIDTA.TB168_4",
descr=
"HU82XDC01ETBU0 orig_bc=GCGCAACG new_bc=GCGCAACG bc_diffs=0",
data=
"GATGAACGCTGACAGAATGCTTAACACATGCAAGTCAACTTGAACTTCGGTTTGGGTGGCGGACGGGTGAGTAACGCGTAAAGAACTTGCCTCACAGCTAGGGACAACATTTGGAAACGAATGCTAATACCTGATATTATGATTATATGGCATCGTATAATTATGAAAGCTATATGCGCTGTGAGAGAGCTTTGCGTCCCATTAGCTAGTTGGAGAGGTAACGGCTCACCAAGGCGATGATGGGTAGCCGGCCTGAGAGGGTGATCGGCCACAAGGGGACTGAGACACGGCCCTTACTCCTACGGGAGGCAGCAGTGGGGGAATATTGGGACAATGGGACCGAGAGTCTGATCCAGCAACTCTGTGTGCACGAT"
),
FASTARecord(
id="PIDTA.TB140_5",
descr=
"HU82XDC01AVWB9 orig_bc=ACTGGAGA new_bc=ACTGGAGA bc_diffs=0",
data=
"GATGAACGCTGACAGAATGCTTAACACATGCAAGTCAACTTGAATTTGGGTTTTAACTTAGATTTGGGTGGCGGACGGGTGAGTAACGCGTAAAGAACTTGCCTCACAGCTAGGGACAACATTTAGAAATGAATGCTAATACCTGATATTATGATTTTAAGGCATCTTAGAATTATGAAAGCTATAAGCACTGTGAGAGAGCTTTGCGTCCCATTAGCTAGTTGGAGAGGTAACAGCTCACCAAGGC"
)
]
for rec1, rec2 in zip(parseFASTA_result, manually_parsed):
self.assertEqual(rec1,
rec2,
msg="FASTA records not parsed as expected.")
def main():
args = handle_program_options()
with open(args.biom_fp, 'rU') as bf:
biom_otus = {row['id'] for row in json.load(bf)['rows']}
repset = util.parseFASTA(args.repset_fp)
seq_ids = set()
with open(args.repset_out_fp, 'w') as out_f:
fasta_str = ">{} {}\n{}\n"
for seq in repset:
if seq.id not in seq_ids and seq.id in biom_otus:
seq_ids.add(seq.id)
out_f.write(fasta_str.format(seq.id, seq.descr, seq.data))
def main():
args = handle_program_options()
with open(args.biom_fp, 'rU') as bf:
biom_otus = {row['id'] for row in json.load(bf)['rows']}
repset = util.parseFASTA(args.repset_fp)
seq_ids = set()
with open(args.repset_out_fp, 'w') as out_f:
fasta_str = ">{} {}\n{}\n"
for seq in repset:
if seq.id not in seq_ids and seq.id in biom_otus:
seq_ids.add(seq.id)
out_f.write(fasta_str.format(seq.id, seq.descr, seq.data))
def test_parseFASTA(self):
"""
Testing parseFASTA function.
:return: Returns OK is test goals were achieved, otherwise raises
error.
"""
FASTARecord = namedtuple("FASTA_Record", "id descr data")
parseFASTA_result = ut.parseFASTA("phylotoast/test/test_FASTA.fna")
manually_parsed = [FASTARecord(id="PIDF154_1", descr="HU82XDC01DBOHO orig_bc=ACAGGTCG new_bc=ACAGGTCG bc_diffs=0", data="AGTGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGGAGATTAAGTAGCTTGCTATTTAATCTTAGTGGCGCACGGGTGAGTAATATATAGCTAATCTGCCCTACACTAGAGGACAACAGTTGGAAACGACTGCTAATACTCTATACTCCTTCTTTACATAAGTTAAGTCGGGAAAGTTTTTCGGTGTAGGATGAGGCTATATCGTATCAGCTAGTGGTAGGTAACGGCCTACCAAGGCTATGACGCGTAACTGGTCTGAGAGGATGATCAGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGGAATATTGCTCAAATGGGGGGAAAACCCTGAAAGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGA"),
FASTARecord(id="PIDTA158_2", descr="HU82XDC01A3N0T orig_bc=ACCGCAGG new_bc=ACCGCAGG bc_diffs=0", data="GATGAACGCTAGCGATAGGCTTAACACATGCAAGTCGAGGGCATCACGAATTAGCAATAGTTTGGTGGCGACCGGCGCACGGGTGCGTAACACGTATACAACCTACCTTCAATTGGGGAATAACCTGGAGAAATTTGGACTAATACCCCATAGTAAACGGGAGAGGCATTCTTTTTTGTTTAAAGATTTATTGATTGGAGATGGGTATGCGTAGGATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATCCTTAGGGGTT"),
FASTARecord(id="PIDF160_3", descr="HU82XDC01DTNIU orig_bc=ACCGTAGA new_bc=ACCGTAGA bc_diffs=0", data="GATGAACGCTGACAGAATGCTTAACACATGCAAGTCTACTTGAACTTCGGTTTGGGTGGCGGACGGGTGAGTAACGCGTAAAGAACTTGCCTCACAGTTAGGGACAACATTTGGAAACGAATGCTAATACCTGATATTATGATTTTAGGGCATCCTAAGATTATGAAAGCTATATGCGCTGTGAGAGAGCTTTGCGTCCCATTAGCTAGTTGGAGAGGTAACGGCTCACCAAGGCGATGATGGGTAGCCGGCCTGAGAGGGTGAACGGGCCACAAGGGGACTGAGACACGGCCCTTACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGACAATGGAACCAAAAGTCTGATCCAGCAATTCTGTGTGCACGATG"),
FASTARecord(id="PIDTA.TB168_4", descr="HU82XDC01ETBU0 orig_bc=GCGCAACG new_bc=GCGCAACG bc_diffs=0", data="GATGAACGCTGACAGAATGCTTAACACATGCAAGTCAACTTGAACTTCGGTTTGGGTGGCGGACGGGTGAGTAACGCGTAAAGAACTTGCCTCACAGCTAGGGACAACATTTGGAAACGAATGCTAATACCTGATATTATGATTATATGGCATCGTATAATTATGAAAGCTATATGCGCTGTGAGAGAGCTTTGCGTCCCATTAGCTAGTTGGAGAGGTAACGGCTCACCAAGGCGATGATGGGTAGCCGGCCTGAGAGGGTGATCGGCCACAAGGGGACTGAGACACGGCCCTTACTCCTACGGGAGGCAGCAGTGGGGGAATATTGGGACAATGGGACCGAGAGTCTGATCCAGCAACTCTGTGTGCACGAT"),
FASTARecord(id="PIDTA.TB140_5", descr="HU82XDC01AVWB9 orig_bc=ACTGGAGA new_bc=ACTGGAGA bc_diffs=0", data="GATGAACGCTGACAGAATGCTTAACACATGCAAGTCAACTTGAATTTGGGTTTTAACTTAGATTTGGGTGGCGGACGGGTGAGTAACGCGTAAAGAACTTGCCTCACAGCTAGGGACAACATTTAGAAATGAATGCTAATACCTGATATTATGATTTTAAGGCATCTTAGAATTATGAAAGCTATAAGCACTGTGAGAGAGCTTTGCGTCCCATTAGCTAGTTGGAGAGGTAACAGCTCACCAAGGC")]
for rec1, rec2 in zip(parseFASTA_result, manually_parsed):
self.assertEqual(
rec1, rec2,
msg="FASTA records not parsed as expected."
)
