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/testaln.stockholm'); 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 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
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/
Email: cjfields-at-uiuc-dot-edu, schattner@alum.mit.edu
Andreas Kahari, ak-at-ebi.ac.uk Jason Stajich, jason-at-bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.