def __add__(self, other):
"""Combines to alignments with the same number of rows by adding them.
If you have two multiple sequence alignments (MSAs), there are two ways to think
about adding them - by row or by column. Using the extend method adds by row.
Using the addition operator adds by column. For example,
>>> from SAP.Bio.Alphabet import generic_dna
>>> from SAP.Bio.Seq import Seq
>>> from SAP.Bio.SeqRecord import SeqRecord
>>> from SAP.Bio.Align import MultipleSeqAlignment
>>> a1 = SeqRecord(Seq("AAAAC", generic_dna), id="Alpha")
>>> b1 = SeqRecord(Seq("AAA-C", generic_dna), id="Beta")
>>> c1 = SeqRecord(Seq("AAAAG", generic_dna), id="Gamma")
>>> a2 = SeqRecord(Seq("GT", generic_dna), id="Alpha")
>>> b2 = SeqRecord(Seq("GT", generic_dna), id="Beta")
>>> c2 = SeqRecord(Seq("GT", generic_dna), id="Gamma")
>>> left = MultipleSeqAlignment([a1, b1, c1],
... annotations={"tool": "demo", "name": "start"})
>>> right = MultipleSeqAlignment([a2, b2, c2],
... annotations={"tool": "demo", "name": "end"})
Now, let's look at these two alignments:
>>> print(left)
DNAAlphabet() alignment with 3 rows and 5 columns
AAAAC Alpha
AAA-C Beta
AAAAG Gamma
>>> print(right)
DNAAlphabet() alignment with 3 rows and 2 columns
GT Alpha
GT Beta
GT Gamma
And add them:
>>> combined = left + right
>>> print(combined)
DNAAlphabet() alignment with 3 rows and 7 columns
AAAACGT Alpha
AAA-CGT Beta
AAAAGGT Gamma
For this to work, both alignments must have the same number of records (here
they both have 3 rows):
>>> len(left)
3
>>> len(right)
3
>>> len(combined)
3
The individual rows are SeqRecord objects, and these can be added together. Refer
to the SeqRecord documentation for details of how the annotation is handled. This
example is a special case in that both original alignments shared the same names,
meaning when the rows are added they also get the same name.
Any common annotations are preserved, but differing annotation is lost. This is
the same behaviour used in the SeqRecord annotations and is designed to prevent
accidental propagation of inappropriate values:
>>> combined.annotations
{'tool': 'demo'}
"""
if not isinstance(other, MultipleSeqAlignment):
raise NotImplementedError
if len(self) != len(other):
raise ValueError("When adding two alignments they must have the same length" " (i.e. same number or rows)")
alpha = Alphabet._consensus_alphabet([self._alphabet, other._alphabet])
merged = (left + right for left, right in zip(self, other))
# Take any common annotation:
annotations = dict()
for k, v in self.annotations.items():
if k in other.annotations and other.annotations[k] == v:
annotations[k] = v
return MultipleSeqAlignment(merged, alpha, annotations)
def __add__(self, other):
"""Combines to alignments with the same number of rows by adding them.
If you have two multiple sequence alignments (MSAs), there are two ways to think
about adding them - by row or by column. Using the extend method adds by row.
Using the addition operator adds by column. For example,
>>> from SAP.Bio.Alphabet import generic_dna
>>> from SAP.Bio.Seq import Seq
>>> from SAP.Bio.SeqRecord import SeqRecord
>>> from SAP.Bio.Align import MultipleSeqAlignment
>>> a1 = SeqRecord(Seq("AAAAC", generic_dna), id="Alpha")
>>> b1 = SeqRecord(Seq("AAA-C", generic_dna), id="Beta")
>>> c1 = SeqRecord(Seq("AAAAG", generic_dna), id="Gamma")
>>> a2 = SeqRecord(Seq("GT", generic_dna), id="Alpha")
>>> b2 = SeqRecord(Seq("GT", generic_dna), id="Beta")
>>> c2 = SeqRecord(Seq("GT", generic_dna), id="Gamma")
>>> left = MultipleSeqAlignment([a1, b1, c1],
... annotations={"tool": "demo", "name": "start"})
>>> right = MultipleSeqAlignment([a2, b2, c2],
... annotations={"tool": "demo", "name": "end"})
Now, let's look at these two alignments:
>>> print(left)
DNAAlphabet() alignment with 3 rows and 5 columns
AAAAC Alpha
AAA-C Beta
AAAAG Gamma
>>> print(right)
DNAAlphabet() alignment with 3 rows and 2 columns
GT Alpha
GT Beta
GT Gamma
And add them:
>>> combined = left + right
>>> print(combined)
DNAAlphabet() alignment with 3 rows and 7 columns
AAAACGT Alpha
AAA-CGT Beta
AAAAGGT Gamma
For this to work, both alignments must have the same number of records (here
they both have 3 rows):
>>> len(left)
3
>>> len(right)
3
>>> len(combined)
3
The individual rows are SeqRecord objects, and these can be added together. Refer
to the SeqRecord documentation for details of how the annotation is handled. This
example is a special case in that both original alignments shared the same names,
meaning when the rows are added they also get the same name.
Any common annotations are preserved, but differing annotation is lost. This is
the same behaviour used in the SeqRecord annotations and is designed to prevent
accidental propagation of inappropriate values:
>>> combined.annotations
{'tool': 'demo'}
"""
if not isinstance(other, MultipleSeqAlignment):
raise NotImplementedError
if len(self) != len(other):
raise ValueError("When adding two alignments they must have the same length"
" (i.e. same number or rows)")
alpha = Alphabet._consensus_alphabet([self._alphabet, other._alphabet])
merged = (left+right for left, right in zip(self, other))
# Take any common annotation:
annotations = dict()
for k, v in self.annotations.items():
if k in other.annotations and other.annotations[k] == v:
annotations[k] = v
return MultipleSeqAlignment(merged, alpha, annotations)
def __init__(self, records, alphabet=None, annotations=None):
"""Initialize a new MultipleSeqAlignment object.
Arguments:
- records - A list (or iterator) of SeqRecord objects, whose
sequences are all the same length. This may be an be an
empty list.
- alphabet - The alphabet for the whole alignment, typically a gapped
alphabet, which should be a super-set of the individual
record alphabets. If omitted, a consensus alphabet is
used.
- annotations - Information about the whole alignment (dictionary).
You would normally load a MSA from a file using Bio.AlignIO, but you
can do this from a list of SeqRecord objects too:
>>> from SAP.Bio.Alphabet import generic_dna
>>> from SAP.Bio.Seq import Seq
>>> from SAP.Bio.SeqRecord import SeqRecord
>>> a = SeqRecord(Seq("AAAACGT", generic_dna), id="Alpha")
>>> b = SeqRecord(Seq("AAA-CGT", generic_dna), id="Beta")
>>> c = SeqRecord(Seq("AAAAGGT", generic_dna), id="Gamma")
>>> align = MultipleSeqAlignment([a, b, c], annotations={"tool": "demo"})
>>> print(align)
DNAAlphabet() alignment with 3 rows and 7 columns
AAAACGT Alpha
AAA-CGT Beta
AAAAGGT Gamma
>>> align.annotations
{'tool': 'demo'}
NOTE - The older Bio.Align.Generic.Alignment class only accepted a
single argument, an alphabet. This is still supported via a backwards
compatible "hack" so as not to disrupt existing scripts and users, but
is deprecated and will be removed in a future release.
"""
if isinstance(records, Alphabet.Alphabet) or isinstance(records, Alphabet.AlphabetEncoder):
if alphabet is None:
# TODO - Remove this backwards compatible mode!
alphabet = records
records = []
import warnings
from SAP.Bio import BiopythonDeprecationWarning
warnings.warn(
"Invalid records argument: While the old "
"Bio.Align.Generic.Alignment class only "
"accepted a single argument (the alphabet), the "
"newer Bio.Align.MultipleSeqAlignment class "
"expects a list/iterator of SeqRecord objects "
"(which can be an empty list) and an optional "
"alphabet argument",
BiopythonDeprecationWarning,
)
else:
raise ValueError("Invalid records argument")
if alphabet is not None:
if not (isinstance(alphabet, Alphabet.Alphabet) or isinstance(alphabet, Alphabet.AlphabetEncoder)):
raise ValueError("Invalid alphabet argument")
self._alphabet = alphabet
else:
# Default while we add sequences, will take a consensus later
self._alphabet = Alphabet.single_letter_alphabet
self._records = []
if records:
self.extend(records)
if alphabet is None:
# No alphabet was given, take a consensus alphabet
self._alphabet = Alphabet._consensus_alphabet(
rec.seq.alphabet for rec in self._records if rec.seq is not None
)
# Annotations about the whole alignment
if annotations is None:
annotations = {}
elif not isinstance(annotations, dict):
raise TypeError("annotations argument should be a dict")
self.annotations = annotations
def __init__(self, records, alphabet=None,
annotations=None):
"""Initialize a new MultipleSeqAlignment object.
Arguments:
- records - A list (or iterator) of SeqRecord objects, whose
sequences are all the same length. This may be an be an
empty list.
- alphabet - The alphabet for the whole alignment, typically a gapped
alphabet, which should be a super-set of the individual
record alphabets. If omitted, a consensus alphabet is
used.
- annotations - Information about the whole alignment (dictionary).
You would normally load a MSA from a file using Bio.AlignIO, but you
can do this from a list of SeqRecord objects too:
>>> from SAP.Bio.Alphabet import generic_dna
>>> from SAP.Bio.Seq import Seq
>>> from SAP.Bio.SeqRecord import SeqRecord
>>> a = SeqRecord(Seq("AAAACGT", generic_dna), id="Alpha")
>>> b = SeqRecord(Seq("AAA-CGT", generic_dna), id="Beta")
>>> c = SeqRecord(Seq("AAAAGGT", generic_dna), id="Gamma")
>>> align = MultipleSeqAlignment([a, b, c], annotations={"tool": "demo"})
>>> print(align)
DNAAlphabet() alignment with 3 rows and 7 columns
AAAACGT Alpha
AAA-CGT Beta
AAAAGGT Gamma
>>> align.annotations
{'tool': 'demo'}
NOTE - The older Bio.Align.Generic.Alignment class only accepted a
single argument, an alphabet. This is still supported via a backwards
compatible "hack" so as not to disrupt existing scripts and users, but
is deprecated and will be removed in a future release.
"""
if isinstance(records, Alphabet.Alphabet) \
or isinstance(records, Alphabet.AlphabetEncoder):
if alphabet is None:
#TODO - Remove this backwards compatible mode!
alphabet = records
records = []
import warnings
from SAP.Bio import BiopythonDeprecationWarning
warnings.warn("Invalid records argument: While the old "
"Bio.Align.Generic.Alignment class only "
"accepted a single argument (the alphabet), the "
"newer Bio.Align.MultipleSeqAlignment class "
"expects a list/iterator of SeqRecord objects "
"(which can be an empty list) and an optional "
"alphabet argument", BiopythonDeprecationWarning)
else :
raise ValueError("Invalid records argument")
if alphabet is not None :
if not (isinstance(alphabet, Alphabet.Alphabet)
or isinstance(alphabet, Alphabet.AlphabetEncoder)):
raise ValueError("Invalid alphabet argument")
self._alphabet = alphabet
else :
#Default while we add sequences, will take a consensus later
self._alphabet = Alphabet.single_letter_alphabet
self._records = []
if records:
self.extend(records)
if alphabet is None:
#No alphabet was given, take a consensus alphabet
self._alphabet = Alphabet._consensus_alphabet(rec.seq.alphabet for
rec in self._records
if rec.seq is not None)
# Annotations about the whole alignment
if annotations is None:
annotations = {}
elif not isinstance(annotations, dict):
raise TypeError("annotations argument should be a dict")
self.annotations = annotations
