Provided by: libbio-perl-perl_1.7.2-2_all bug


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


         # 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/');
         while( my $aln = $in->next_aln ) {



       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

         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

         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
            AC        accession
            ID        id
            DE        description

           Tag        Bio::Annotation   TagName                    Parameters
            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
            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 =>
           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);


           # 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);


           # STOCKHOLM 1.0

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


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

       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:

AUTHORS - Chris Fields, Peter Schattner

       Email: cjfields-at-uiuc-dot-edu,


       Andreas Kahari, Jason Stajich,


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

        Title   : new
        Usage   : my $alignio = Bio::AlignIO->new(-format => 'stockholm'
                                                 -file   => '>file');
        Function: Initialize a new L<Bio::AlignIO::stockholm> 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.

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

        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

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

        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)

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