Package Bio :: Package AlignIO :: Module StockholmIO
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Module StockholmIO

source code


Bio.AlignIO support for the "stockholm" format (used in the PFAM database).

You are expected to use this module via the Bio.AlignIO functions (or the
Bio.SeqIO functions if you want to work directly with the gapped sequences).

For example, consider a Stockholm alignment file containing the following:

    # STOCKHOLM 1.0
    #=GC SS_cons       .................<<<<<<<<...<<<<<<<........>>>>>>>..
    AP001509.1         UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGU
    #=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..--
    AE007476.1         AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGU
    #=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>----

    #=GC SS_cons       ......<<<<<<<.......>>>>>>>..>>>>>>>>...............
    AP001509.1         CUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
    #=GR AP001509.1 SS -------<<<<<--------->>>>>--->>>>>>>>---------------
    AE007476.1         UUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
    #=GR AE007476.1 SS ------.<<<<<--------->>>>>.-->>>>>>>>---------------
    //

This is a single multiple sequence alignment, so you would probably load this
using the Bio.AlignIO.read() function:

    >>> from Bio import AlignIO
    >>> handle = open("Stockholm/simple.sth", "rU")
    >>> align = AlignIO.read(handle, "stockholm")
    >>> handle.close()
    >>> print align
    SingleLetterAlphabet() alignment with 2 rows and 104 columns
    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-G...UGU AP001509.1
    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-C...GAU AE007476.1
    >>> for record in align :
    ...     print record.id, len(record)
    AP001509.1 104
    AE007476.1 104

This example file is clearly using RNA, so you might want the Alignment object
(and the SeqRecord objects it holds) to reflect this, rather than simple using
the default single letter alphabet as shown above.  You can do this with an
optional argument to the Bio.AlignIO.read() function:

    >>> from Bio import AlignIO
    >>> from Bio.Alphabet import generic_rna
    >>> handle = open("Stockholm/simple.sth", "rU")
    >>> align = AlignIO.read(handle, "stockholm", alphabet=generic_rna)
    >>> handle.close()
    >>> print align
    RNAAlphabet() alignment with 2 rows and 104 columns
    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-G...UGU AP001509.1
    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-C...GAU AE007476.1

In addition to the sequences themselves, this example alignment also includes
some GR lines for the secondary structure of the sequences.  These are strings,
with one character for each letter in the associated sequence:

    >>> for record in align :
    ...     print record.id
    ...     print record.seq
    ...     print record.letter_annotations['secondary_structure']
    AP001509.1
    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
    -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>---------------
    AE007476.1
    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
    -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>---------------

Any general annotation for each row is recorded in the SeqRecord's annotations
dictionary.  You can output this alignment in many different file formats using
Bio.AlignIO.write(), or the Alignment object's format method:

    >>> print align.format("fasta")
    >AP001509.1
    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-A
    GGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
    >AE007476.1
    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAA
    GGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
    <BLANKLINE>

Most output formats won't be able to hold the annotation possible in a Stockholm file:

    >>> print align.format("stockholm")
    # STOCKHOLM 1.0
    #=GF SQ 2
    AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
    #=GS AP001509.1 AC AP001509.1
    #=GS AP001509.1 DE AP001509.1
    #=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>---------------
    AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
    #=GS AE007476.1 AC AE007476.1
    #=GS AE007476.1 DE AE007476.1
    #=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>---------------
    //
    <BLANKLINE>

Note that when writing Stockholm files, Biopython does not break long sequences up and
interleave them (as in the input file shown above).  The standard allows this simpler
layout, and it is more likely to be understood by other tools. 
    
Finally, as an aside, it can sometimes be useful to use Bio.SeqIO.parse() to iterate over
the two rows as SeqRecord objects - rather than working with Alignnment objects.
Again, if you want to you can specify this is RNA:

    >>> from Bio import SeqIO
    >>> from Bio.Alphabet import generic_rna
    >>> handle = open("Stockholm/simple.sth", "rU")
    >>> for record in SeqIO.parse(handle, "stockholm", alphabet=generic_rna) :
    ...     print record.id
    ...     print record.seq
    ...     print record.letter_annotations['secondary_structure']
    AP001509.1
    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
    -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>---------------
    AE007476.1
    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
    -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>---------------
    >>> handle.close()

Classes [hide private]
  StockholmWriter
Stockholm/PFAM alignment writer.
  StockholmIterator
Loads a Stockholm file from PFAM into Alignment objects.
Functions [hide private]
 
_test()
Run the Bio.SeqIO module's doctests.
source code
Function Details [hide private]

_test()

source code 

Run the Bio.SeqIO module's doctests.

This will try and locate the unit tests directory, and run the doctests from there in order that the relative paths used in the examples work.