Bio::AlignIO::stockholm(3)

NAME
Bio::AlignIO::stockholm - stockholm sequence input/output stream

SYNOPSIS
  # Do not use this module directly.  Use it via the L<Bio::AlignIO> class.

  use Bio::AlignIO;
  use strict;

  my $in = Bio::AlignIO->new(-format => 'stockholm',
                             -file   => 't/data/testaln.stockholm');
  while( my $aln = $in->next_aln ) {

  }

DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from stockholm flat file databases. This has been completely refactored from the original stockholm parser to handle annotation data and now includes a write_aln() method for (almost) complete stockholm format output.

Stockholm alignment records normally contain additional sequence-based and alignment-based annotation

  GF Lines (alignment feature/annotation):
  #=GF <featurename> <Generic per-file annotation, free text>
  Placed above the alignment

  GC Lines (Alignment consensus)
  #=GC <featurename> <Generic per-column annotation, exactly 1
       character per column>
  Placed below the alignment

  GS Lines (Sequence annotations)
  #=GS <seqname> <featurename> <Generic per-sequence annotation, free
       text>

  GR Lines (Sequence meta data)
  #=GR <seqname> <featurename> <Generic per-sequence AND per-column
       mark up, exactly 1 character per column>

Currently, sequence annotations (those designated with GS tags) are parsed only for accession numbers and descriptions. It is intended that full parsing will be added at some point in the near future along with a builder option for optionally parsing alignment annotation and meta data.

The following methods/tags are currently used for storing and writing the alignment annotation data.

    Tag        SimpleAlign
                 Method
    ----------------------------------------------------------------------
     AC        accession
     ID        id
     DE        description
    ----------------------------------------------------------------------

    Tag        Bio::Annotation   TagName                    Parameters
               Class
    ----------------------------------------------------------------------
     AU        SimpleValue       record_authors             value
     SE        SimpleValue       seed_source                value
     GA        SimpleValue       gathering_threshold        value
     NC        SimpleValue       noise_cutoff               value
     TC        SimpleValue       trusted_cutoff             value
     TP        SimpleValue       entry_type                 value
     SQ        SimpleValue       num_sequences              value
     PI        SimpleValue       previous_ids               value
     DC        Comment           database_comment           comment
     CC        Comment           alignment_comment          comment
     DR        Target            dblink                     database
                                                            primary_id
                                                            comment
     AM        SimpleValue       build_method               value
     NE        SimpleValue       pfam_family_accession      value
     NL        SimpleValue       sequence_start_stop        value
     SS        SimpleValue       sec_structure_source       value
     BM        SimpleValue       build_model                value
     RN        Reference         reference                  *
     RC        Reference         reference                  comment
     RM        Reference         reference                  pubmed
     RT        Reference         reference                  title
     RA        Reference         reference                  authors
     RL        Reference         reference                  location
    ----------------------------------------------------------------------
  * RN is generated based on the number of Bio::Annotation::Reference objects

  Custom annotation
Some users may want to add custom annotation beyond those mapped above. Currently there are two methods to do so; however, the methods used for adding such annotation may change in the future, particularly if alignment Writer classes are introduced. In particular, do not rely on changing the global variables @WRITEORDER or %WRITEMAP as these may be made private at some point.

1) Use (and abuse) the 'custom' tag. The tagname for the object can differ from the tagname used to store the object in the AnnotationCollection.

    # AnnotationCollection from the SimpleAlign object
    my $coll = $aln->annotation;
    my $factory = Bio::Annotation::AnnotationFactory->new(-type =>
        Bio::Annotation::SimpleValue');
    my $rfann = $factory->create_object(-value => $str,
                                        -tagname => 'mytag');
    $coll->add_Annotation('custom', $rfann);
    $rfann = $factory->create_object(-value => 'foo',
                                    -tagname => 'bar');
    $coll->add_Annotation('custom', $rfann);

OUTPUT:

    # STOCKHOLM 1.0

    #=GF ID myID12345
    #=GF mytag katnayygqelggvnhdyddlakfyfgaglealdffnnkeaaakiinwvaEDTTRGKIQDLV??
    #=GF mytag TPtd~????LDPETQALLV???????????????????????NAIYFKGRWE?????????~??
    #=GF mytag ??HEF?A?EMDTKPY??DFQH?TNen?????GRI??????V???KVAM??MF?????????N??
    #=GF mytag ???DD?VFGYAEL????DE???????L??D??????A??TALELAY??????????????????
    #=GF mytag ?????????????KG??????Sa???TSMLILLP???????????????D??????????????
    #=GF mytag ???????????EGTr?????AGLGKLLQ??QL????????SREef??DLNK??L???AH????R
    #=GF mytag ????????????L????????????????????????????????????????R?????????R
    #=GF mytag ??QQ???????V???????AVRLPKFSFefefdlkeplknlgmhqafdpnsdvfklmdqavlvi
    #=GF mytag gdlqhayafkvd????????????????????????????????????????????????????
    #=GF mytag ????????????????????????????????????????????????????????????????
    #=GF mytag ????????????????????????????????????????????????????????????????
    #=GF mytag ????????????????????????????????????????????????????????????????
    #=GF mytag ?????????????INVDEAG?TEAAAATAAKFVPLSLppkt??????????????????PIEFV
    #=GF mytag ADRPFAFAIR??????E?PAT?G????SILFIGHVEDPTP?msv?
    #=GF bar foo
    ...

2) Modify the global @WRITEORDER and %WRITEMAP.

    # AnnotationCollection from the SimpleAlign object
    my $coll = $aln->annotation;

    # add to WRITEORDER
    my @order = @Bio::AlignIO::stockholm::WRITEORDER;
    push @order, 'my_stuff';
    @Bio::AlignIO::stockholm::WRITEORDER = @order;

    # make sure new tag maps to something
    $Bio::AlignIO::stockholm::WRITEMAP{my_stuff} = 'Hobbit/SimpleValue';

    my $rfann = $factory->create_object(-value => 'Frodo',
                                        -tagname => 'Hobbit');
    $coll->add_Annotation('my_stuff', $rfann);
    $rfann = $factory->create_object(-value => 'Bilbo',
                                     -tagname => 'Hobbit');
    $coll->add_Annotation('my_stuff', $rfann);

OUTPUT:

    # STOCKHOLM 1.0

    #=GF ID myID12345
    #=GF Hobbit Frodo
    #=GF Hobbit Bilbo
    ....

FEEDBACK

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHORS - Chris Fields, Peter Schattner
Email: cjfields-at-uiuc-dot-edu, schattner@alum.mit.edu

CONTRIBUTORS
Andreas Kahari, ak-at-ebi.ac.uk Jason Stajich, jason-at-bioperl.org

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 Title   : new
 Usage   : my $alignio = Bio::AlignIO->new(-format => 'phylip'
                                          -file   => '>file');
 Function: Initialize a new L<Bio::AlignIO::phylip> reader or writer
 Returns : L<Bio::AlignIO> object
 Args    : -line_length :  length of the line for the alignment block
           -alphabet    :  symbol alphabet to set the sequences to.  If not set,
                           the parser will try to guess based on the alignment
                           accession (if present), defaulting to 'dna'.
           -spaces      :  (optional, def = 1) boolean to add a space in between
                           the "# STOCKHOLM 1.0" header and the annotation and
                           the annotation and the alignment.

  next_aln
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : L<Bio::Align::AlignI> object
 Args    : NONE

  write_aln
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in stockholm format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object

  line_length
 Title   : line_length
 Usage   : $obj->line_length($newval)
 Function: Set the alignment output line length
 Returns : value of line_length
 Args    : newvalue (optional)

  alphabet
 Title   : alphabet
 Usage   : $obj->alphabet('dna')
 Function: Set the sequence data alphabet
 Returns : sequence data type
 Args    : newvalue (optional)

  spaces
 Title   : spaces
 Usage   : $obj->spaces(1)
 Function: Set the 'spaces' flag, which prints extra newlines between the
           header and the annotation and the annotation and the alignment
 Returns : sequence data type
 Args    : newvalue (optional)

  alignhandler
 Title   : alignhandler
 Usage   : $stream->alignhandler($handler)
 Function: Get/Set the Bio::HandlerBaseI object
 Returns : Bio::HandlerBaseI
 Args    : Bio::HandlerBaseI