def load_one_file(args, cxn, file_name, ends, seq_end_clamp=''):
"""Load sequences from a fasta/fastq file into the atram database."""
log.info('Loading "{}" into sqlite database'.format(file_name))
parser = get_parser(args, file_name)
with util.open_file(args, file_name) as sra_file:
batch = []
for rec in parser(sra_file):
title = rec[0].strip()
seq = rec[1]
seq_name, seq_end = blast.parse_fasta_title(
title, ends, seq_end_clamp)
batch.append((seq_name, seq_end, seq))
if len(batch) >= db.BATCH_SIZE:
db.insert_sequences_batch(cxn, batch)
batch = []
db.insert_sequences_batch(cxn, batch)
def load_one_file(args, cxn, file_name, ends, seq_end_clamp=''):
"""Load sequences from a fasta/fastq file into the atram database."""
log.info('Loading "{}" into sqlite database'.format(file_name))
parser = get_parser(args, file_name)
with util.open_file(args, file_name) as sra_file:
batch = []
for rec in parser(sra_file):
title = rec[0].strip()
seq = rec[1]
seq_name, seq_end = blast.parse_fasta_title(
title, ends, seq_end_clamp)
batch.append((seq_name, seq_end, seq))
if len(batch) >= db.BATCH_SIZE:
db.insert_sequences_batch(cxn, batch)
batch = []
db.insert_sequences_batch(cxn, batch)
def test_parse_fasta_title_10():
"""It handles single ends with no sequence end."""
seq_name, seq_end = blast.parse_fasta_title('title after', 'single_ends',
'')
assert seq_name == 'title'
assert seq_end == ''
def test_parse_fasta_title_09():
"""It handles mixed ends with a space delimited sequence end."""
seq_name, seq_end = blast.parse_fasta_title('title 2 after', 'mixed_ends',
'')
assert seq_name == 'title'
assert seq_end == '2'
def test_parse_fasta_title_07():
"""It handles mixed ends with no sequence end."""
seq_name, seq_end = blast.parse_fasta_title('title', 'mixed_ends', '')
assert seq_name == 'title'
assert seq_end == ''
def test_parse_fasta_title_06():
"""It handles a dot delimited end."""
seq_name, seq_end = blast.parse_fasta_title('title.1 after', 'end_1', '1')
assert seq_name == 'title'
assert seq_end == '1'
def test_parse_fasta_title_05():
"""It handles an underscore delimited end."""
seq_name, seq_end = blast.parse_fasta_title('title_1', 'end_1', '1')
assert seq_name == 'title'
assert seq_end == '1'
def test_parse_fasta_title_04():
"""It handles a slash delimited end."""
seq_name, seq_end = blast.parse_fasta_title(
'title/2 after', 'end_2', '2')
assert seq_name == 'title'
assert seq_end == '2'
def test_parse_fasta_title_01():
"""It handles empty strings."""
actual_seq_name, actual_seq_end = blast.parse_fasta_title('', '', '')
assert actual_seq_name == ''
assert actual_seq_end == ''
def test_parse_fasta_title_12():
"""It handles single ends with a space delimited sequence end."""
seq_name, seq_end = blast.parse_fasta_title(
'title 2 words', 'single_ends', '')
assert seq_name == 'title'
assert seq_end == ''
def test_parse_fasta_title_10():
"""It handles single ends with no sequence end."""
seq_name, seq_end = blast.parse_fasta_title(
'title after', 'single_ends', '')
assert seq_name == 'title'
assert seq_end == ''
def test_parse_fasta_title_09():
"""It handles mixed ends with a space delimited sequence end."""
seq_name, seq_end = blast.parse_fasta_title(
'title 2 after', 'mixed_ends', '')
assert seq_name == 'title'
assert seq_end == '2'
def test_parse_fasta_title_07():
"""It handles mixed ends with no sequence end."""
seq_name, seq_end = blast.parse_fasta_title(
'title', 'mixed_ends', '')
assert seq_name == 'title'
assert seq_end == ''
def test_parse_fasta_title_06():
"""It handles a dot delimited end."""
seq_name, seq_end = blast.parse_fasta_title(
'title.1 after', 'end_1', '1')
assert seq_name == 'title'
assert seq_end == '1'
def test_parse_fasta_title_05():
"""It handles an underscore delimited end."""
seq_name, seq_end = blast.parse_fasta_title(
'title_1', 'end_1', '1')
assert seq_name == 'title'
assert seq_end == '1'
def test_parse_fasta_title_01():
"""It handles empty strings."""
actual_seq_name, actual_seq_end = blast.parse_fasta_title('', '', '')
assert actual_seq_name == ''
assert actual_seq_end == ''
def test_parse_fasta_title_12():
"""It handles single ends with a space delimited sequence end."""
seq_name, seq_end = blast.parse_fasta_title('title 2 words', 'single_ends',
'')
assert seq_name == 'title 2'
assert seq_end == ''
def test_parse_fasta_title_03():
"""It handles a 1 or 2 at the end of the title."""
seq_name, seq_end = blast.parse_fasta_title('title1/2 after', 'end_2', '2')
assert seq_name == 'title1'
assert seq_end == '2'
def test_parse_fasta_title_04():
"""It handles a slash delimited end."""
seq_name, seq_end = blast.parse_fasta_title('title/2 after', 'end_2', '2')
assert seq_name == 'title'
assert seq_end == '2'
def test_parse_fasta_title_03():
"""It handles a 1 or 2 at the end of the title."""
seq_name, seq_end = blast.parse_fasta_title(
'title1/2 after', 'end_2', '2')
assert seq_name == 'title1'
assert seq_end == '2'