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

       Bio::AlignIO::arp - ARP MSA Sequence input/output stream

       Do not use this module directly.	 Use it	via the	Bio::AlignIO class.

       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:

       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
	   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

       Please direct usage questions or	support	issues to the mailing list:

       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

       Chris Fields (cjfields)

       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	: 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

	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 v5.32.1			  2019-12-07		  Bio::AlignIO::arp(3)


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