def to_alignment(sequences, alphabet=None, strict=True):
"""Returns a multiple sequence alignment (OBSOLETE).
- sequences -An iterator that returns SeqRecord objects,
or simply a list of SeqRecord objects. All
the record sequences must be the same length.
- alphabet - Optional alphabet. Stongly recommended.
- strict - Optional, defaults to True. Should error checking
be done?
Using this function is now discouraged. Rather doing this:
>>> from Bio import SeqIO
>>> handle = open("Clustalw/protein.aln")
>>> alignment = SeqIO.to_alignment(SeqIO.parse(handle, "clustal"))
>>> handle.close()
You are now encouraged to use Bio.AlignIO instead, e.g.
>>> from Bio import AlignIO
>>> handle = open("Clustalw/protein.aln")
>>> alignment = AlignIO.read(handle, "clustal")
>>> handle.close()
"""
#TODO - Move this functionality into the Alignment class instead?
from Bio.Alphabet import generic_alphabet
from Bio.Alphabet import _consensus_alphabet
if alphabet is None:
sequences = list(sequences)
alphabet = _consensus_alphabet([rec.seq.alphabet for rec in sequences \
if rec.seq is not None])
if not (isinstance(alphabet, Alphabet) or isinstance(alphabet, AlphabetEncoder)):
raise ValueError("Invalid alphabet")
alignment_length = None
alignment = Alignment(alphabet)
for record in sequences:
if strict:
if alignment_length is None:
alignment_length = len(record.seq)
elif alignment_length != len(record.seq):
raise ValueError("Sequences must all be the same length")
assert isinstance(record.seq.alphabet, Alphabet) \
or isinstance(record.seq.alphabet, AlphabetEncoder), \
"Sequence does not have a valid alphabet"
#TODO - Move this alphabet comparison code into the Alphabet module/class?
#TODO - Is a normal alphabet "ungapped" by default, or does it just mean
#undecided?
if isinstance(record.seq.alphabet, Alphabet) \
and isinstance(alphabet, Alphabet):
#Comparing two non-gapped alphabets
if not isinstance(record.seq.alphabet, alphabet.__class__):
raise ValueError("Incompatible sequence alphabet " \
+ "%s for %s alignment" \
% (record.seq.alphabet, alphabet))
elif isinstance(record.seq.alphabet, AlphabetEncoder) \
and isinstance(alphabet, Alphabet):
raise ValueError("Sequence has a gapped alphabet, alignment does not")
elif isinstance(record.seq.alphabet, Alphabet) \
and isinstance(alphabet, Gapped):
#Sequence isn't gapped, alignment is.
if not isinstance(record.seq.alphabet, alphabet.alphabet.__class__):
raise ValueError("Incompatible sequence alphabet " \
+ "%s for %s alignment" \
% (record.seq.alphabet, alphabet))
else:
#Comparing two gapped alphabets
if not isinstance(record.seq.alphabet, alphabet.__class__):
raise ValueError("Incompatible sequence alphabet " \
+ "%s for %s alignment" \
% (record.seq.alphabet, alphabet))
if record.seq.alphabet.gap_char != alphabet.gap_char:
raise ValueError("Sequence gap characters != alignment gap char")
#ToDo, additional checks on the specified alignment...
#Should we look at the alphabet.contains() method?
if record.seq is None:
raise TypeError("SeqRecord (id=%s) has None for its sequence." % record.id)
#This is abusing the "private" records list,
#we should really have a method like add_sequence
#but which takes SeqRecord objects. See also Bug 1944
alignment._records.append(record)
return alignment
def to_alignment(sequences, alphabet=None, strict=True):
"""Returns a multiple sequence alignment (OBSOLETE).
- sequences -An iterator that returns SeqRecord objects,
or simply a list of SeqRecord objects. All
the record sequences must be the same length.
- alphabet - Optional alphabet. Stongly recommended.
- strict - Optional, defaults to True. Should error checking
be done?
Using this function is now discouraged. Rather doing this:
>>> from Bio import SeqIO
>>> handle = open("Clustalw/protein.aln")
>>> alignment = SeqIO.to_alignment(SeqIO.parse(handle, "clustal"))
>>> handle.close()
You are now encouraged to use Bio.AlignIO instead, e.g.
>>> from Bio import AlignIO
>>> handle = open("Clustalw/protein.aln")
>>> alignment = AlignIO.read(handle, "clustal")
>>> handle.close()
"""
#TODO - Move this functionality into the Alignment class instead?
from Bio.Alphabet import generic_alphabet
from Bio.Alphabet import _consensus_alphabet
if alphabet is None:
sequences = list(sequences)
alphabet = _consensus_alphabet([rec.seq.alphabet for rec in sequences \
if rec.seq is not None])
if not (isinstance(alphabet, Alphabet)
or isinstance(alphabet, AlphabetEncoder)):
raise ValueError("Invalid alphabet")
alignment_length = None
alignment = Alignment(alphabet)
for record in sequences:
if strict:
if alignment_length is None:
alignment_length = len(record.seq)
elif alignment_length != len(record.seq):
raise ValueError("Sequences must all be the same length")
assert isinstance(record.seq.alphabet, Alphabet) \
or isinstance(record.seq.alphabet, AlphabetEncoder), \
"Sequence does not have a valid alphabet"
#TODO - Move this alphabet comparison code into the Alphabet module/class?
#TODO - Is a normal alphabet "ungapped" by default, or does it just mean
#undecided?
if isinstance(record.seq.alphabet, Alphabet) \
and isinstance(alphabet, Alphabet):
#Comparing two non-gapped alphabets
if not isinstance(record.seq.alphabet, alphabet.__class__):
raise ValueError("Incompatible sequence alphabet " \
+ "%s for %s alignment" \
% (record.seq.alphabet, alphabet))
elif isinstance(record.seq.alphabet, AlphabetEncoder) \
and isinstance(alphabet, Alphabet):
raise ValueError(
"Sequence has a gapped alphabet, alignment does not")
elif isinstance(record.seq.alphabet, Alphabet) \
and isinstance(alphabet, Gapped):
#Sequence isn't gapped, alignment is.
if not isinstance(record.seq.alphabet,
alphabet.alphabet.__class__):
raise ValueError("Incompatible sequence alphabet " \
+ "%s for %s alignment" \
% (record.seq.alphabet, alphabet))
else:
#Comparing two gapped alphabets
if not isinstance(record.seq.alphabet, alphabet.__class__):
raise ValueError("Incompatible sequence alphabet " \
+ "%s for %s alignment" \
% (record.seq.alphabet, alphabet))
if record.seq.alphabet.gap_char != alphabet.gap_char:
raise ValueError(
"Sequence gap characters != alignment gap char")
#ToDo, additional checks on the specified alignment...
#Should we look at the alphabet.contains() method?
if record.seq is None:
raise TypeError("SeqRecord (id=%s) has None for its sequence." %
record.id)
#This is abusing the "private" records list,
#we should really have a method like add_sequence
#but which takes SeqRecord objects. See also Bug 1944
alignment._records.append(record)
return alignment