def __format__(self, format_spec):
"""Returns the alignment as a string in the specified file format.
This method supports the python format() function added in
Python 2.6/3.0. The format_spec should be a lower case
string supported by Bio.AlignIO as an output file format.
See also the alignment's format() method."""
if format_spec:
from SAP.Bio._py3k import StringIO
from SAP.Bio import AlignIO
handle = StringIO()
AlignIO.write([self], handle, format_spec)
return handle.getvalue()
else:
#Follow python convention and default to using __str__
return str(self)
def write(sequences, handle, format):
"""Write complete set of sequences to a file.
- sequences - A list (or iterator) of SeqRecord objects, or (if using
Biopython 1.54 or later) a single SeqRecord.
- handle - File handle object to write to, or filename as string
(note older versions of Biopython only took a handle).
- format - lower case string describing the file format to write.
You should close the handle after calling this function.
Returns the number of records written (as an integer).
"""
from SAP.Bio import AlignIO
#Try and give helpful error messages:
if not isinstance(format, basestring):
raise TypeError("Need a string for the file format (lower case)")
if not format:
raise ValueError("Format required (lower case string)")
if format != format.lower():
raise ValueError("Format string '%s' should be lower case" % format)
if isinstance(sequences, SeqRecord):
#This raised an exception in order version of Biopython
sequences = [sequences]
if format in _BinaryFormats:
mode = 'wb'
else:
mode = 'w'
with as_handle(handle, mode) as fp:
#Map the file format to a writer class
if format in _FormatToWriter:
writer_class = _FormatToWriter[format]
count = writer_class(fp).write_file(sequences)
elif format in AlignIO._FormatToWriter:
#Try and turn all the records into a single alignment,
#and write that using Bio.AlignIO
alignment = MultipleSeqAlignment(sequences)
alignment_count = AlignIO.write([alignment], fp, format)
assert alignment_count == 1, \
"Internal error - the underlying writer " \
" should have returned 1, not %s" % repr(alignment_count)
count = len(alignment)
del alignment_count, alignment
elif format in _FormatToIterator or format in AlignIO._FormatToIterator:
raise ValueError("Reading format '%s' is supported, but not writing"
% format)
else:
raise ValueError("Unknown format '%s'" % format)
assert isinstance(count, int), "Internal error - the underlying %s " \
"writer should have returned the record count, not %s" \
% (format, repr(count))
return count
def write(sequences, handle, format):
"""Write complete set of sequences to a file.
- sequences - A list (or iterator) of SeqRecord objects, or (if using
Biopython 1.54 or later) a single SeqRecord.
- handle - File handle object to write to, or filename as string
(note older versions of Biopython only took a handle).
- format - lower case string describing the file format to write.
You should close the handle after calling this function.
Returns the number of records written (as an integer).
"""
from SAP.Bio import AlignIO
#Try and give helpful error messages:
if not isinstance(format, basestring):
raise TypeError("Need a string for the file format (lower case)")
if not format:
raise ValueError("Format required (lower case string)")
if format != format.lower():
raise ValueError("Format string '%s' should be lower case" % format)
if isinstance(sequences, SeqRecord):
#This raised an exception in order version of Biopython
sequences = [sequences]
if format in _BinaryFormats:
mode = 'wb'
else:
mode = 'w'
with as_handle(handle, mode) as fp:
#Map the file format to a writer class
if format in _FormatToWriter:
writer_class = _FormatToWriter[format]
count = writer_class(fp).write_file(sequences)
elif format in AlignIO._FormatToWriter:
#Try and turn all the records into a single alignment,
#and write that using Bio.AlignIO
alignment = MultipleSeqAlignment(sequences)
alignment_count = AlignIO.write([alignment], fp, format)
assert alignment_count == 1, \
"Internal error - the underlying writer " \
" should have returned 1, not %s" % repr(alignment_count)
count = len(alignment)
del alignment_count, alignment
elif format in _FormatToIterator or format in AlignIO._FormatToIterator:
raise ValueError(
"Reading format '%s' is supported, but not writing" % format)
else:
raise ValueError("Unknown format '%s'" % format)
assert isinstance(count, int), "Internal error - the underlying %s " \
"writer should have returned the record count, not %s" \
% (format, repr(count))
return count
