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Bio::AlignIO::bl2seq(3User Contributed Perl DocumentatiBio::AlignIO::bl2seq(3)

NAME
       Bio::AlignIO::bl2seq - bl2seq sequence input/output stream

SYNOPSIS
       Do not use this module directly.	 Use it	via the	Bio::AlignIO class, as
       in:

	   use Bio::AlignIO;

	   $in	= Bio::AlignIO->new(-file   => "inputfilename" ,
				    -format => "bl2seq",
				    -report_type => "blastn");
	   $aln	= $in->next_aln();

DESCRIPTION
       This object can create Bio::SimpleAlign sequence	alignment objects (of
       two sequences) from "bl2seq" BLAST reports.

       A nice feature of this module is	that - in combination with
       Bio::Tools::Run::StandAloneBlast.pm or a	remote BLAST - it can be used
       to align	two sequences and make a Bio::SimpleAlign object from them
       which can then be manipulated using any Bio::SimpleAlign	methods, eg:

	  # Get	two sequences
	  $str = Bio::SeqIO->new(-file=>'t/amino.fa' , '-format' => 'Fasta', );
	  my $seq3 = $str->next_seq();
	  my $seq4 = $str->next_seq();

	  # Run	bl2seq on them
	  $factory = Bio::Tools::StandAloneBlast->new('program'	=> 'blastp',
						      'outfile'	=> 'bl2seq.out');
	  my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
	  # Note that report is	a Bio::SearchIO	object

	  # Use	AlignIO.pm to create a SimpleAlign object from the bl2seq report
	  $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
	  $aln = $str->next_aln();

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   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://github.com/bioperl/bioperl-live/issues

AUTHOR - Peter Schattner
       Email: schattner@alum.mit.edu

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	Title	: new
	Usage	: my $alignio =	Bio::SimpleAlign->new(-format => 'bl2seq',
						      -file   => 'filename',
						      -report_type => 'blastx');
	Function: Get a	L<Bio::SimpleAlign>
	Returns	: L<Bio::SimpleAlign> object
	Args	: -report_type => report type (blastn,blastx,tblastx,tblastn,blastp)

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln()
	Function: returns the next alignment in	the stream.
	Returns	: L<Bio::Align::AlignI>	object on success,
		  undef	on error or end	of file
	Args	: none

   write_aln (NOT IMPLEMENTED)
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: writes the $aln object into the stream in bl2seq format
	Returns	: 1 for	success	and 0 for error
	Args	: L<Bio::Align::AlignI>	object

   report_type
	Title	: report_type
	Usage	: $obj->report_type($newval)
	Function: Sets the report type (blastn,	blastp...)
	Returns	: value	of report_type (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

perl v5.32.1			  2019-12-07	       Bio::AlignIO::bl2seq(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Peter Schattner | APPENDIX

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