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Bio::AlignIO::stockholm.3pm

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        DBLink            aln_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
 
 

FEEDBACK

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 _

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