def seqio(in_fhands, out_fhands, out_format, copy_if_same_format=True):
'It converts sequence files between formats'
in_formats = [guess_format(fhand) for fhand in in_fhands]
if (len(in_formats) == 1 and in_formats[0] == out_format and
hasattr(in_fhands[0], 'name')):
if copy_if_same_format:
copyfileobj(in_fhands[0], out_fhands[0])
else:
rel_symlink(in_fhands[0].name, out_fhands[0].name)
elif len(in_fhands) == 1 and len(out_fhands) == 1:
try:
SeqIO.convert(in_fhands[0], in_formats[0], out_fhands[0],
out_format)
except ValueError as error:
if error_quality_disagree(error):
raise MalformedFile(str(error))
raise
elif (len(in_fhands) == 1 and len(out_fhands) == 2 and
out_format == 'fasta'):
try:
for seq in read_seqrecords([in_fhands[0]]):
SeqIO.write([seq], out_fhands[0], out_format)
SeqIO.write([seq], out_fhands[1], 'qual')
except ValueError, error:
if error_quality_disagree(error):
raise MalformedFile(str(error))
raise
def seqio(in_fhands, out_fhand, out_format, copy_if_same_format=True):
'It converts sequence files between formats'
if out_format not in get_setting('SUPPORTED_OUTPUT_FORMATS'):
raise IncompatibleFormatError("This output format is not supported")
in_formats = [remove_multiline(guess_format(fhand)) for fhand in in_fhands]
if len(in_fhands) == 1 and in_formats[0] == out_format:
if copy_if_same_format:
copyfileobj(in_fhands[0], out_fhand)
else:
rel_symlink(in_fhands[0].name, out_fhand.name)
else:
seqs = _read_seqrecords(in_fhands)
try:
write_seqrecs(seqs, out_fhand, out_format)
except ValueError, error:
if error_quality_disagree(error):
raise MalformedFile(str(error))
if 'No suitable quality scores' in str(error):
msg = 'No qualities available to write output file'
raise IncompatibleFormatError(msg)
raise
def seqio(in_fhands, out_fhand, out_format, copy_if_same_format=True):
'It converts sequence files between formats'
if out_format not in get_setting('SUPPORTED_OUTPUT_FORMATS'):
raise IncompatibleFormatError("This output format is not supported")
in_formats = [get_format(fhand) for fhand in in_fhands]
if len(in_fhands) == 1 and in_formats[0] == out_format:
if copy_if_same_format:
copyfileobj(in_fhands[0], out_fhand)
else:
rel_symlink(in_fhands[0].name, out_fhand.name)
else:
seqs = _read_seqrecords(in_fhands)
try:
write_seqrecs(seqs, out_fhand, out_format)
except ValueError, error:
if error_quality_disagree(error):
raise MalformedFile(str(error))
if 'No suitable quality scores' in str(error):
msg = 'No qualities available to write output file'
raise IncompatibleFormatError(msg)
raise
def test_rel_symlink(self):
'It tests various cases of rel symlinks'
tempdir = TemporaryDir()
try:
hola = os.path.join(tempdir.name, 'hola')
os.mkdir(hola)
caracola = os.path.join(tempdir.name, 'caracola')
rel_symlink(hola, caracola)
assert os.path.exists(caracola)
fname = os.path.join(hola, 'fname')
open(fname, 'w')
caracola2 = os.path.join(tempdir.name, 'caracola2')
rel_symlink(fname, caracola2)
assert os.path.exists(caracola2)
path2 = os.path.join(tempdir.name, 'dir1', 'dir2')
os.makedirs(path2)
caracola3 = os.path.join(path2, 'caracola3')
rel_symlink(hola, caracola3)
assert os.path.exists(caracola3)
finally:
tempdir.close()
def test_rel_symlink(self):
'It tests various cases of rel symlinks'
tempdir = TemporaryDir()
try:
hola = os.path.join(tempdir.name, 'hola')
os.mkdir(hola)
caracola = os.path.join(tempdir.name, 'caracola')
rel_symlink(hola, caracola)
assert os.path.exists(caracola)
fname = os.path.join(hola, 'fname')
open(fname, 'w')
caracola2 = os.path.join(tempdir.name, 'caracola2')
rel_symlink(fname, caracola2)
assert os.path.exists(caracola2)
path2 = os.path.join(tempdir.name, 'dir1', 'dir2')
os.makedirs(path2)
caracola3 = os.path.join(path2, 'caracola3')
rel_symlink(hola, caracola3)
assert os.path.exists(caracola3)
finally:
tempdir.close()
def test_rel_symlink(self):
"It tests various cases of rel symlinks"
tempdir = TemporaryDir()
try:
hola = os.path.join(tempdir.name, "hola")
os.mkdir(hola)
caracola = os.path.join(tempdir.name, "caracola")
rel_symlink(hola, caracola)
assert os.path.exists(caracola)
fname = os.path.join(hola, "fname")
open(fname, "w")
caracola2 = os.path.join(tempdir.name, "caracola2")
rel_symlink(fname, caracola2)
assert os.path.exists(caracola2)
path2 = os.path.join(tempdir.name, "dir1", "dir2")
os.makedirs(path2)
caracola3 = os.path.join(path2, "caracola3")
rel_symlink(hola, caracola3)
assert os.path.exists(caracola3)
finally:
tempdir.close()
in_formats == ['fasta', 'qual']):
seq_records = SeqIO.QualityIO.PairedFastaQualIterator(in_fhands[0],
in_fhands[1])
try:
SeqIO.write(seq_records, out_fhands[0].name, out_format)
except ValueError, error:
if error_quality_disagree(error):
raise MalformedFile(str(error))
raise
elif (len(in_fhands) == 2 and len(out_fhands) == 2 and
in_formats == ['fasta', 'qual'] and out_format == 'fasta'):
if copy_if_same_format:
copyfileobj(in_fhands[0], out_fhands[0])
copyfileobj(in_fhands[1], out_fhands[1])
else:
rel_symlink(in_fhands[0].name, out_fhands[0].name)
rel_symlink(in_fhands[1].name, out_fhands[1].name)
else:
raise RuntimeError('Please fixme, we should not be here')
for out_fhand in out_fhands:
out_fhand.flush()
def _count_seqs_in_fasta(fhand):
'It counts the seqs in a fasta file'
count = 0
for line in fhand:
if line[0] == '>':
count += 1
return count
