Package Bio :: Package Align :: Module Generic :: Class Alignment
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Class Alignment

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Known Subclasses:

Represent a set of alignments.

This is a base class to represent alignments, which can be subclassed to deal with an alignment in a specific format.

Instance Methods [hide private]
 
__format__(self, format_spec)
Returns the alignment as a string in the specified file format.
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__getitem__(self, index)
Access part of the alignment.
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__init__(self, alphabet)
Initialize a new Alignment object.
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__iter__(self)
Iterate over alignment rows as SeqRecord objects.
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__len__(self)
Returns the number of sequences in the alignment.
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__repr__(self)
Returns a representation of the object for debugging.
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__str__(self)
Returns a multi-line string summary of the alignment.
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_str_line(self, record)
Returns a truncated string representation of a SeqRecord (PRIVATE).
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add_sequence(self, descriptor, sequence, start=None, end=None, weight=1.0)
Add a sequence to the alignment.
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format(self, format)
Returns the alignment as a string in the specified file format.
source code
 
get_alignment_length(self)
Return the maximum length of the alignment.
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get_all_seqs(self)
Return all of the sequences involved in the alignment.
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get_column(self, col)
Returns a string containing a given column.
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get_seq_by_num(self, number)
Retrieve a sequence by row number (OBSOLETE).
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Method Details [hide private]

__format__(self, format_spec)

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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.

__getitem__(self, index)
(Indexing operator)

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Access part of the alignment.

We'll use the following example alignment here for illustration:

>>> from Bio.Alphabet import IUPAC, Gapped
>>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))
>>> align.add_sequence("Alpha",  "ACTGCTAGCTAG")
>>> align.add_sequence("Beta",   "ACT-CTAGCTAG")
>>> align.add_sequence("Gamma",  "ACTGCTAGATAG")
>>> align.add_sequence("Delta",  "ACTGCTTGCTAG")
>>> align.add_sequence("Epsilon","ACTGCTTGATAG")

You can access a row of the alignment as a SeqRecord using an integer index (think of the alignment as a list of SeqRecord objects here):

>>> first_record = align[0]
>>> print first_record.id, first_record.seq
Alpha ACTGCTAGCTAG
>>> last_record = align[-1]
>>> print last_record.id, last_record.seq
Epsilon ACTGCTTGATAG

You can also access use python's slice notation to create a sub-alignment containing only some of the SeqRecord objects:

>>> sub_alignment = align[2:5]
>>> print sub_alignment
Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns
ACTGCTAGATAG Gamma
ACTGCTTGCTAG Delta
ACTGCTTGATAG Epsilon

This includes support for a step, i.e. align[start:end:step], which can be used to select every second sequence:

>>> sub_alignment = align[::2]
>>> print sub_alignment
Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns
ACTGCTAGCTAG Alpha
ACTGCTAGATAG Gamma
ACTGCTTGATAG Epsilon

Or to get a copy of the alignment with the rows in reverse order:

>>> rev_alignment = align[::-1]
>>> print rev_alignment
Gapped(IUPACUnambiguousDNA(), '-') alignment with 5 rows and 12 columns
ACTGCTTGATAG Epsilon
ACTGCTTGCTAG Delta
ACTGCTAGATAG Gamma
ACT-CTAGCTAG Beta
ACTGCTAGCTAG Alpha

Right now, these are the ONLY indexing operations supported. The use of a second column based index is under discussion for a future update.

__init__(self, alphabet)
(Constructor)

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Initialize a new Alignment object.

Arguments: o alphabet - The alphabet to use for the sequence objects that are created. This alphabet must be a gapped type.

e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGATAG Gamma

__iter__(self)

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Iterate over alignment rows as SeqRecord objects.

e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> for record in align: ... print record.id ... print record.seq Alpha ACTGCTAGCTAG Beta ACT-CTAGCTAG Gamma ACTGCTAGATAG

__len__(self)
(Length operator)

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Returns the number of sequences in the alignment.

Use len(alignment) to get the number of sequences (i.e. the number of rows), and alignment.get_alignment_length() to get the length of the longest sequence (i.e. the number of columns).

This is easy to remember if you think of the alignment as being like a list of SeqRecord objects.

__repr__(self)
(Representation operator)

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Returns a representation of the object for debugging.

The representation cannot be used with eval() to recreate the object, which is usually possible with simple python ojects. For example:

<Bio.Align.Generic.Alignment instance (2 records of length 14, SingleLetterAlphabet()) at a3c184c>

The hex string is the memory address of the object, see help(id). This provides a simple way to visually distinguish alignments of the same size.

__str__(self)
(Informal representation operator)

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Returns a multi-line string summary of the alignment.

This output is intended to be readable, but large alignments are shown truncated. A maximum of 20 rows (sequences) and 50 columns are shown, with the record identifiers. This should fit nicely on a single screen. e.g.

>>> from Bio.Alphabet import IUPAC, Gapped
>>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))
>>> align.add_sequence("Alpha", "ACTGCTAGCTAG")
>>> align.add_sequence("Beta",  "ACT-CTAGCTAG")
>>> align.add_sequence("Gamma", "ACTGCTAGATAG")
>>> print align
Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns
ACTGCTAGCTAG Alpha
ACT-CTAGCTAG Beta
ACTGCTAGATAG Gamma

See also the alignment's format method.

_str_line(self, record)

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Returns a truncated string representation of a SeqRecord (PRIVATE).

This is a PRIVATE function used by the __str__ method.

add_sequence(self, descriptor, sequence, start=None, end=None, weight=1.0)

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Add a sequence to the alignment.

This doesn't do any kind of alignment, it just adds in the sequence
object, which is assumed to be prealigned with the existing
sequences.

Arguments:
o descriptor - The descriptive id of the sequence being added.
               This will be used as the resulting SeqRecord's
               .id property (and, for historical compatibility,
               also the .description property)
o sequence - A string with sequence info.
o start - You can explicitly set the start point of the sequence.
This is useful (at least) for BLAST alignments, which can just
be partial alignments of sequences.
o end - Specify the end of the sequence, which is important
for the same reason as the start.
o weight - The weight to place on the sequence in the alignment.
By default, all sequences have the same weight. (0.0 => no weight,
1.0 => highest weight)

format(self, format)

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Returns the alignment as a string in the specified file format.

The format should be a lower case string supported as an output
format by Bio.AlignIO (such as "fasta", "clustal", "phylip",
"stockholm", etc), which is used to turn the alignment into a
string.

e.g.
>>> from Bio.Alphabet import IUPAC, Gapped
>>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))
>>> align.add_sequence("Alpha", "ACTGCTAGCTAG")
>>> align.add_sequence("Beta",  "ACT-CTAGCTAG")
>>> align.add_sequence("Gamma", "ACTGCTAGATAG")
>>> print align.format("fasta")
>Alpha
ACTGCTAGCTAG
>Beta
ACT-CTAGCTAG
>Gamma
ACTGCTAGATAG
<BLANKLINE>
>>> print align.format("phylip")
 3 12
Alpha      ACTGCTAGCT AG
Beta       ACT-CTAGCT AG
Gamma      ACTGCTAGAT AG
<BLANKLINE>

For Python 2.6, 3.0 or later see also the built in format() function.

get_alignment_length(self)

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Return the maximum length of the alignment.

All objects in the alignment should (hopefully) have the same length. This function will go through and find this length by finding the maximum length of sequences in the alignment.

>>> from Bio.Alphabet import IUPAC, Gapped
>>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))
>>> align.add_sequence("Alpha", "ACTGCTAGCTAG")
>>> align.add_sequence("Beta",  "ACT-CTAGCTAG")
>>> align.add_sequence("Gamma", "ACTGCTAGATAG")
>>> align.get_alignment_length()
12

If you want to know the number of sequences in the alignment, use len(align) instead:

>>> len(align)
3

get_all_seqs(self)

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Return all of the sequences involved in the alignment.

The return value is a list of SeqRecord objects.

This method is semi-obsolete, as the Alignment object itself offers much of the functionality of a list of SeqRecord objects (e.g. iteration or slicing to create a sub-alignment).

get_column(self, col)

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Returns a string containing a given column.

e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> align.get_column(0) 'AAA' >>> align.get_column(3) 'G-G'

get_seq_by_num(self, number)

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Retrieve a sequence by row number (OBSOLETE).

Returns:
o A Seq object for the requested sequence.

Raises:
o IndexError - If the specified number is out of range.

NOTE: This is a legacy method.  In new code where you need to access
the rows of the alignment (i.e. the sequences) consider iterating
over them or accessing them as SeqRecord objects.  e.g.

for record in alignment:
    print record.id
    print record.seq
first_record = alignment[0]
last_record = alignment[-1]