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Bio::SearchIO::blast_pUser3Contributed Perl DocumeBio::SearchIO::blast_pull(3)

NAME
       Bio::SearchIO::blast_pull - A parser for	BLAST output

SYNOPSIS
	   # do	not use	this class directly it is available through Bio::SearchIO
	   use Bio::SearchIO;
	   my $in = Bio::SearchIO->new(-format => 'blast_pull',
				      -file   => 't/data/new_blastn.txt');
	   while (my $result = $in->next_result) {
	       # this is a Bio::Search::Result::BlastPullResult	object
	       print "Results for ", $result->query_name(), "\n";
	       while (my $hit =	$result->next_hit) {
		   print $hit->name(), "\n";
		   while (my $hsp = $hit->next_hsp) {
		       print "length is	", $hsp->length(), "\n";
		   }
	       }
	   }

DESCRIPTION
       This object implements a	pull-parser for	BLAST output. It is fast since
       it only does work on request (hence 'pull').

       Currently only NCBI BLASTN and BLASTP are supported.

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 the
       Bioperl mailing list.  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 of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

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

   new
	Title	: new
	Usage	: my $obj = Bio::SearchIO::blast_pull->new();
	Function: Builds a new Bio::SearchIO::blast_pull object
	Returns	: Bio::SearchIO::blast_pull
	Args	: -fh/-file => BLAST output filename
		  -format   => 'blast_pull'
		  -evalue   => float or	scientific notation number to be used
			       as an evalue cutoff for hits
		  -score    => integer or scientific notation number to	be used
			       as a score value	cutoff for hits
		  -piped_behaviour => 'temp_file'|'memory'|'sequential_read'

		  -piped_behaviour defines what	the parser should do if	the input is
		   an unseekable filehandle (eg. piped input), see
		   Bio::PullParserI::chunk for details.	Default	is 'memory'.

   next_result
	Title	: next_result
	Usage	: my $hit = $searchio->next_result;
	Function: Returns the next Result from a search
	Returns	: Bio::Search::Result::ResultI object
	Args	: none

   result_count
	Title	: result_count
	Usage	: my $count = $searchio->result_count
	Function: Returns the number of	results	we have	processed.
	Returns	: integer
	Args	: none

   rewind
	Title	: rewind
	Usage	: $searchio->rewind;
	Function: Allow	one to reset the Result	iterator to the	beginning, so that
		  next_result()	will subsequently return the first result and so on.

		  NB: result objects are not cached, so	you will get new result	objects
		  each time you	rewind.	Also, note that	result_count() counts the
		  number of times you have called next_result(), so will not be	able
		  tell you how many results there were in the file if you use rewind().

	Returns	: n/a
	Args	: none

perl v5.32.1			  2019-12-07	  Bio::SearchIO::blast_pull(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sendu Bala | APPENDIX

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