Bio.AlignIO support for “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::

AP001509.1         UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGU

AE007476.1         AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGU



AP001509.1         CUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU

AE007476.1         UUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU

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

     >>> from Bio import AlignIO
     >>> align = AlignIO.read("Stockholm/simple.sth", "stockholm")
     >>> 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("%s %i" % (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
     >>> align = AlignIO.read("Stockholm/simple.sth", "stockholm",
     ...                      alphabet=generic_rna)
     >>> 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. Any per-column annotation for the entire alignment in in the alignment’s column annotations dictionary, such as the secondary structure consensus in this example:

     >>> sorted(align.column_annotations.keys())
     ['secondary_structure']
     >>> align.column_annotations["secondary_structure"]
     '.................<<<<<<<<...<<<<<<<........>>>>>>>........<<<<<<<.......>>>>>>>..>>>>>>>>...............'

You can output this alignment in many different file formats using Bio.AlignIO.write(), or the MultipleSeqAlignment 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"))


AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU



AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU




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Note that when writing Stockholm files, AlignIO 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 alignment 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
     >>> for record in SeqIO.parse("Stockholm/simple.sth", "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
     -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>---------------

Remember that if you slice a SeqRecord, the per-letter-annotations like the secondary structure string here, are also sliced:

     >>> sub_record = record[10:20]
     >>> print(sub_record.seq)
     AUCGUUUUAC
     >>> print(sub_record.letter_annotations['secondary_structure'])
     -------<<<

Likewise with the alignment object, as long as you are not dropping any rows, slicing specific columns of an alignment will slice any per-column-annotations:

     >>> align.column_annotations["secondary_structure"]
     '.................<<<<<<<<...<<<<<<<........>>>>>>>........<<<<<<<.......>>>>>>>..>>>>>>>>...............'
     >>> part_align = align[:,10:20]
     >>> part_align.column_annotations["secondary_structure"]
     '.......<<<'

You can also see this in the Stockholm output of this partial-alignment:

     >>> print(part_align.format("stockholm"))


AP001509.1 UCAACACUCU



AE007476.1 AUCGUUUUAC




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