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)