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AMEN: v.1.1.2 released, four changes & three bugs fixed !
07-25-2008
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Bio::AlignIO::arp(3pm) User Contributed Perl Documentation Bio::AlignIO::arp(3pm) NAME
Bio::AlignIO::arp - ARP MSA Sequence input/output stream SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class. DESCRIPTION
This object can create Bio::SimpleAlign objects from ARP flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: http://lgb.unige.ch/arlequin/ For the moment, this retains the allele sequence data in the DATA section and inserts them into SimpleAlign objects. ARP files that contain other data (RFLP, etc.) are not expected to parse properly. Also, if the DNA data is actually SNP data, then the LocatableSeq object instantiation will throw an error. This is now set up as a generic parser (i.e. it parses everything) and collects as much data as possible into the SimpleAlign object. The following in a general mapping of where data can be found: Tag SimpleAlign Method ---------------------------------------------------------------------- Title description SampleName id ---------------------------------------------------------------------- Tag Bio::Annotation TagName Bio::Annotation Class Parameters ---------------------------------------------------------------------- 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 * ---------------------------------------------------------------------- * RN is generated based on the number of Bio::Annotation::Reference objects In addition, the number of samples found in the alignment is retained in a Bio::Annotation::TagTree object in the annotation collection and is accessible via: ($samples) = $aln->annotation->get_Annotations('Samples'); say $samples->display_text; # or use other relevant TagTree methods to retrieve data 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: https://redmine.open-bio.org/projects/bioperl/ AUTHORS
Chris Fields (cjfields) 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 : Bio::Align::AlignI object - returns 0 on end of file or on error Args : -width => optional argument to specify the width sequence will be written (60 chars by default) See Bio::Align::AlignI write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in xmfa format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object See Bio::Align::AlignI perl v5.14.2 2012-03-02 Bio::AlignIO::arp(3pm)