def test_write_fasta_sequence1(nucseq, tmpdir):
seq_id, seq = next(fasta.load_fasta(nucseq))
file_name = (tmpdir / 'test.fa').strpath
file_handle = open_file(file_name, 'w')
fasta.write_fasta_sequence(file_handle, seq_id, seq)
file_handle.close()
seq_idw, seqw = next(fasta.load_fasta(file_name))
assert (seq_id, seq) == (seq_idw, seqw)
def test_write_fasta_sequence2(nucseq, tmpdir):
file_name = (tmpdir / 'test.fa').strpath
file_handle = open_file(file_name, 'w')
for seq_id, seq in fasta.load_fasta(nucseq):
fasta.write_fasta_sequence(file_handle, seq_id, seq)
file_handle.close()
count1 = sum(1 for x in fasta.load_fasta(nucseq))
count2 = sum(1 for x in fasta.load_fasta(file_name))
assert count1 == count2
def filter_command(verbose, len_gt, len_lt, header_contains, seq_pattern, wrap, fasta_file, output_file):
"""
.. versionadded:: 0.5.7
Filters a fasta file
"""
mgkit.logger.config_log(level=logging.DEBUG if verbose else logging.INFO)
if wrap:
wrap = 60
else:
wrap = None
for name, seq in fasta.load_fasta(fasta_file):
seq_len = len(seq)
if len_gt is not None:
if not (seq_len > len_gt):
continue
if len_lt is not None:
if not (seq_len < len_lt):
continue
if header_contains is not None:
if header_contains not in name:
continue
if seq_pattern is not None:
if seq_pattern not in seq:
continue
fasta.write_fasta_sequence(output_file, name, seq, wrap=wrap)
def translate_command(verbose, trans_table, one_seq, no_wrap, progress, fasta_file, output_file):
mgkit.logger.config_log(level=logging.DEBUG if verbose else logging.INFO)
if one_seq:
LOG.info("Assuming the sequences are in the correct frame")
LOG.info(
'Writing to file (%s)',
getattr(output_file, 'name', repr(output_file))
)
trans_table = load_trans_table(trans_table)
iterator = fasta.load_fasta(fasta_file)
if progress:
iterator = tqdm(iterator)
if no_wrap:
wrap = None
else:
wrap = 60
for name, seq in iterator:
if one_seq:
new_seq = translate_sequence(seq, 0, trans_table, False)
fasta.write_fasta_sequence(output_file, name, new_seq, wrap=wrap)
else:
for new_header, new_seq in translate_seq(name, seq, trans_table):
fasta.write_fasta_sequence(output_file, new_header, new_seq, wrap=wrap)
def infer_parameters(file_handle, fastq_bool, progress):
LOG.info("Extrapolating model from file %s", file_handle.name)
if fastq_bool:
it = load_fastq(file_handle, num_qual=True)
quals = []
else:
it = fasta.load_fasta(file_handle)
if progress:
it = tqdm(it)
gc_content = []
length = 0
for record in it:
length = max(length, len(record[1]))
gc_content.append(sequence.sequence_gc_content(record[1]))
if fastq_bool:
quals.append(record[2])
if fastq_bool:
model = sequence.extrapolate_model(quals)
else:
model = None
gc_content = numpy.mean(gc_content)
return length, gc_content, model
def sequence_command(verbose, reverse, no_wrap, split, reference, progress,
gff_file, fasta_file):
mgkit.logger.config_log(level=logging.DEBUG if verbose else logging.INFO)
if reference is None:
utils.exit_script('A fasta reference file is required', 1)
wrap = 60
if no_wrap:
wrap = None
seqs = dict((seq_id.split(' ')[0] if split else seq_id, seq)
for seq_id, seq in fasta.load_fasta(reference))
ann_iter = gff.parse_gff(gff_file, gff_type=gff.from_gff)
seq_iter = gff.extract_nuc_seqs(ann_iter, seqs, reverse=reverse)
if progress:
seq_iter = tqdm(seq_iter)
for name, seq in seq_iter:
fasta.write_fasta_sequence(fasta_file, name, seq, wrap=wrap)
def get_aa_data(f_handle):
"""
Load aminoacid seuqnces used by HMMER.
"""
# LOG.info('Loading aa data from file %s', f_handle.name)
aa_seqs = dict(
(name.split(' ')[0], seq) for name, seq in fasta.load_fasta(f_handle))
return aa_seqs
def test_split_fasta_file2(nucseq, tmpdir):
fasta.split_fasta_file(nucseq, (tmpdir / 'test{}.fa').strpath, 3)
files = list(
str(path) for path in pathlib.Path(tmpdir.strpath).glob('*.fa'))
count1 = sum(1 for x in fasta.load_fasta(nucseq))
count2 = sum(1 for x in fasta.load_fasta_files(files))
assert count1 == count2
def uid_command(verbose, table, fasta_file, output_file):
mgkit.logger.config_log(level=logging.DEBUG if verbose else logging.INFO)
if table is not None:
LOG.info(
'Writing Table to file (%s)',
getattr(table, 'name', repr(table))
)
LOG.info(
'Writing to file (%s)',
getattr(output_file, 'name', repr(output_file))
)
for name, seq in fasta.load_fasta(fasta_file):
uid = str(uuid4())
if table is not None:
table.write("{}\t{}\n".format(uid, name).encode('ascii'))
fasta.write_fasta_sequence(output_file, uid, seq)
def test_load_fasta5(oneseq):
seq_id, seq = next(fasta.load_fasta(oneseq))
assert len(seq) == 630
def test_load_fasta4(oneseq):
count = sum(1 for x in fasta.load_fasta(oneseq))
assert count == 1
def test_load_fasta3(nucseq):
count = sum(1 for x in fasta.load_fasta(nucseq))
assert count == 115
def test_load_fasta2(nucseq):
seq_id, seq = next(fasta.load_fasta(nucseq))
assert seq_id == u'contig-1467318'
def test_load_fasta1(nucseq):
seq_id, seq = next(fasta.load_fasta(nucseq))
assert seq == u'ATCGATGTCTGCCGCAATGACGGTGGCACCACGCTGGGCAGAGCGTACGACGGCACCCATACCGACCATGCCACAGCCAATCACCATGACGACATCGATATCTGTTACCTGGGCACGACTGACAGCATGGAAACCCACACTCATCGGTTCGATTAATGCACAGGTGCGGGGTGTCAGCAGTCCTGCGGGGATGACTTTCTCCCAGGGCAGGGCGAGATACTCACACATGGCTCCCCAGCGCTGCACACCTAATGTCTGGTTGTGCTCGCAGGCATTGACACGGTCGTTACGGCATGACGCACATTTTCCACAGTTGGTGTAGGGGTTGACGGTGACGGTCATACCGGGCTTCAGTCCCTCAGGTACGTTCTTGCCAATCTTGACAATCTCCGCACCTACCTCATGACCGGGAACCACAGGCATCTTCACCATCGGGTTACCGCCACGGAAGGTATTCAGGTCACTGCCGCAAAAACC'
def nucseq(shared_datadir):
return dict(
fasta.load_fasta(str(shared_datadir / 'test-seq-nuc.fa'))
)
def aaseq(shared_datadir):
return dict(
fasta.load_fasta(str(shared_datadir / 'test-seq-aa.fa'))
)
