def writeMSA(filename, msa, **kwargs):
"""Returns *filename* containing *msa*, a :class:`.MSA` or :class:`.MSAFile`
instance, in the specified *format*, which can be *SELEX*, *Stockholm*, or
*FASTA*. If *compressed* is **True** or *filename* ends with :file:`.gz`,
a compressed file will be written. :class:`.MSA` instances will be written
using C function into uncompressed files.
Can also write *CLUSTAL* or *PIR* format files using Python functions."""
fntemp, ext = splitext(filename)
ext = ext.lower()
compressed = kwargs.get('compressed', ext == '.gz')
if compressed and ext != '.gz':
filename += '.gz'
format = kwargs.get('format', None)
if format:
try:
format = MSAFORMATS[format.lower()]
except KeyError:
raise ValueError('format {0} is not recognized'
.format(repr(format)))
else:
if ext == '.gz':
ext = splitext(fntemp)[1].lower()
try:
format = MSAEXTMAP[ext]
except KeyError:
raise ValueError('format is not specified, and file extension '
'{0} is not recognized'.format(repr(ext)))
fast = False
try:
seqarr, _, _ = msa._getArray(), msa.numResidues(), msa.numSequences()
except AttributeError:
try:
msa.getFormat(), msa.getFilename(), msa.getFilter()
except AttributeError:
raise ValueError('msa must be an MSA or MSAFile instance, not {0}'
.format(type(msa).__name__))
else:
seqiter = msa
else:
seqiter = msa
fast = True
if not fast or compressed:
with MSAFile(filename, 'w', format=format) as out:
write = out.write
[write(seq) for seq in seqiter]
else:
from prody.utilities import backupFile
backupFile(filename)
if format == FASTA:
from .msaio import writeFasta
writeFasta(filename, msa._labels, seqarr,
kwargs.get('line_length', LEN_FASTA_LINE))
elif format == CLUSTAL:
writeClustal(filename, msa)
elif format == PIR:
writePIR(filename, msa, **kwargs)
else:
from .msaio import writeSelex
writeSelex(filename, msa._labels, seqarr,
stockholm=format != SELEX,
label_length=kwargs.get('label_length',
LEN_SELEX_LABEL))
return filename
def writeMSA(filename, msa, **kwargs):
"""Returns *filename* containing *msa*, a :class:`.MSA` or :class:`.MSAFile`
instance, in the specified *format*, which can be *SELEX*, *Stockholm*, or
*FASTA*. If *compressed* is **True** or *filename* ends with :file:`.gz`,
a compressed file will be written. :class:`.MSA` instances will be written
using C function into uncompressed files."""
fntemp, ext = splitext(filename)
ext = ext.lower()
compressed = kwargs.get('compressed', ext == '.gz')
if compressed and ext != '.gz':
filename += '.gz'
format = kwargs.get('format', None)
if format:
try:
format = MSAFORMATS[format.lower()]
except KeyError:
raise ValueError('format {0} is not recognized'
.format(repr(format)))
else:
if ext == '.gz':
ext = splitext(fntemp)[1].lower()
try:
format = MSAEXTMAP[ext]
except KeyError:
raise ValueError('format is not specified, and file extension '
'{0} is not recognized'.format(repr(ext)))
fast = False
try:
seqarr, _, _ = msa._getArray(), msa.numResidues(), msa.numSequences()
except AttributeError:
try:
msa.getFormat(), msa.getFilename(), msa.getFilter()
except AttributeError:
raise ValueError('msa must be an MSA or MSAFile instance, not '
.format(type(msa).__name__))
else:
seqiter = msa
else:
seqiter = msa
fast = True
if not fast or compressed:
with MSAFile(filename, 'w', format=format) as out:
write = out.write
[write(seq) for seq in seqiter]
else:
from prody.utilities import backupFile
backupFile(filename)
if format == FASTA:
from .msaio import writeFasta
writeFasta(filename, msa._labels, seqarr,
kwargs.get('line_length', LEN_FASTA_LINE))
else:
from .msaio import writeSelex
writeSelex(filename, msa._labels, seqarr,
stockholm=format != SELEX,
label_length=kwargs.get('label_length',
LEN_SELEX_LABEL))
return filename