Class Alignment

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

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.

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.

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.

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.

Return all of the sequences involved in the alignment (DEPRECATED).

The return value is a list of SeqRecord objects.

This method is deprecated, as the Alignment object itself now offers
much of the functionality of a list of SeqRecord objects (e.g.
iteration or slicing to create a sub-alignment). Instead use the
Python builtin function list, i.e. my_list = list(my_align)

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

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]

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.

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

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)

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'

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.