def read_sequences(filename, qualities=False, genbank_callback=None):
""" Read fasta or illumina sequences, possibly compressed
Valid values for qualities: False,True,'required'
Post reading filters can be applied.
"""
assert qualities in (False,True,'required')
parts = filename.split('~~')
info = get_file_info(parts[0])
have_qualities = False
if 'type-empty' in info:
have_qualities = True
result = read_empty(parts[0])
elif 'type-fasta' in info:
result = read_fasta(parts[0])
elif 'type-genbank' in info:
result = read_genbank_sequence(parts[0], genbank_callback)
elif 'type-fastq' in info:
have_qualities = True
result = read_illumina_with_quality(parts[0])
elif 'type-gff' in info:
result = read_gff3_sequence(parts[0])
elif 'type-sff' in info:
f.close()
grace.require_sff2fastq()
have_qualities = True
process = run(['sff2fastq', parts[0]])
result = read_illumina_with_quality(process.stdout)
else:
raise grace.Error('Unrecognized file format for '+filename)
if qualities == 'required' and not have_qualities:
raise grace.Error('Need base qualities in '+filename)
for part in parts[1:]:
for prefix in FILTERS:
if part.lower().startswith(prefix):
result = FILTERS[prefix](result, part[len(prefix):])
break
else:
raise grace.Error('Unrecognized filter: '+part)
if have_qualities and not qualities:
result = filter_no_qualities(result)
return result
def read_sequences(filename, qualities=False, genbank_callback=None):
""" Read fasta or illumina sequences, possibly compressed
Valid values for qualities: False,True,'required'
Post reading filters can be applied.
"""
assert qualities in (False, True, 'required')
parts = filename.split('~~')
info = get_file_info(parts[0])
have_qualities = False
if 'type-empty' in info:
have_qualities = True
result = read_empty(parts[0])
elif 'type-fasta' in info:
result = read_fasta(parts[0])
elif 'type-genbank' in info:
result = read_genbank_sequence(parts[0], genbank_callback)
elif 'type-fastq' in info:
have_qualities = True
result = read_illumina_with_quality(parts[0])
elif 'type-gff' in info:
result = read_gff3_sequence(parts[0])
elif 'type-sff' in info:
f.close()
grace.require_sff2fastq()
have_qualities = True
process = run(['sff2fastq', parts[0]])
result = read_illumina_with_quality(process.stdout)
else:
raise grace.Error('Unrecognized file format for ' + filename)
if qualities == 'required' and not have_qualities:
raise grace.Error('Need base qualities in ' + filename)
for part in parts[1:]:
for prefix in FILTERS:
if part.lower().startswith(prefix):
result = FILTERS[prefix](result, part[len(prefix):])
break
else:
raise grace.Error('Unrecognized filter: ' + part)
if have_qualities and not qualities:
result = filter_no_qualities(result)
return result
def read_sequences(filename, qualities=False, genbank_callback=None):
""" Read fasta or illumina sequences, possibly compressed
Post reading filters can be applied.
"""
parts = filename.split('~~')
f = open_possibly_compressed_file(parts[0])
peek = f.read(8)
f.close()
have_qualities = False
if not peek:
result = read_empty(parts[0])
elif peek.startswith('>'):
result = read_fasta(parts[0])
elif peek.startswith('LOCUS'):
result = read_genbank_sequence(parts[0], genbank_callback)
elif peek.startswith('@'):
have_qualities = True
result = read_illumina_with_quality(parts[0])
elif peek.startswith('##gff'):
result = read_gff3_sequence(parts[0])
elif peek.startswith('.sff'):
f.close()
grace.require_sff2fastq()
have_qualities = True
process = run(['sff2fastq', parts[0]])
result = read_illumina_with_quality(process.stdout)
else:
raise grace.Error('Unrecognized file format for ' + filename)
for part in parts[1:]:
for prefix in FILTERS:
if part.lower().startswith(prefix):
result = FILTERS[prefix](result, part[len(prefix):])
break
else:
raise grace.Error('Unrecognized filter: ' + part)
if have_qualities and not qualities:
result = filter_no_qualities(result)
return result
def read_sequences(filename, qualities=False, genbank_callback=None):
""" Read fasta or illumina sequences, possibly compressed
Post reading filters can be applied.
"""
parts = filename.split('~~')
f = open_possibly_compressed_file(parts[0])
peek = f.read(8)
f.close()
have_qualities = False
if not peek:
result = read_empty(parts[0])
elif peek.startswith('>'):
result = read_fasta(parts[0])
elif peek.startswith('LOCUS'):
result = read_genbank_sequence(parts[0], genbank_callback)
elif peek.startswith('@'):
have_qualities = True
result = read_illumina_with_quality(parts[0])
elif peek.startswith('##gff'):
result = read_gff3_sequence(parts[0])
elif peek.startswith('.sff'):
f.close()
grace.require_sff2fastq()
have_qualities = True
process = run(['sff2fastq', parts[0]])
result = read_illumina_with_quality(process.stdout)
else:
raise grace.Error('Unrecognized file format for '+filename)
for part in parts[1:]:
for prefix in FILTERS:
if part.lower().startswith(prefix):
result = FILTERS[prefix](result, part[len(prefix):])
break
else:
raise grace.Error('Unrecognized filter: '+part)
if have_qualities and not qualities:
result = filter_no_qualities(result)
return result
