Bio::AlignIO::arp man page on Pidora

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Bio::AlignIO::arp(3)  User Contributed Perl Documentation Bio::AlignIO::arp(3)

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:

	 http://bugzilla.open-bio.org/

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 v5.14.1			  2011-07-22		  Bio::AlignIO::arp(3)
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