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Bio::Tools::BPlite::Iteration.3pm
Langue: en
Version: 2008-06-24 (ubuntu - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::BPlite::Iteration - object for parsing single iteration of a PSIBLAST reportSYNOPSIS
use Bio::Tools::BPpsilite; open my $FH, "t/psiblastreport.out"; $report = Bio::Tools::BPpsilite->new(-fh=>\*FH); # determine number of iterations executed by psiblast $total_iterations = $report->number_of_iterations; $last_iteration = $report->round($total_iterations); # Process only hits found in last iteration ... $oldhitarray_ref = $last_iteration->oldhits; HIT: while($sbjct = $last_iteration->nextSbjct) { $id = $sbjct->name; $is_old = grep /\Q$id\E/, @$oldhitarray_ref; if ($is_old ){next HIT;} # do something with new hit... }
ALIGNMENTS
# This assumed that you have $db pointing to a database, $out to an output file # $slxdir to a directory and $psiout # note the alignments can only be obtained if the flag "-m 6" is run. # It might also be necessary to use the flag -v to get all alignments # my @psiparams = ('database' => $db , 'output' => $out, 'j' => 3, 'm' => 6, 'h' => 1.e-3 , 'F' => 'T' , 'Q' => $psiout ); my $factory = Bio::Tools::Run::StandAloneBlast->new(@psiparams); my $report = $factory->blastpgp($seq); my $total_iterations = $report->number_of_iterations(); my $last_iteration = $report->round($total_iterations); my $align=$last_iteration->Align; my $slxfile=$slxdir.$id.".slx"; my $slx = Bio::AlignIO->new('-format' => 'selex','-file' => ">".$slxfile ); $slx->write_aln($align);
DESCRIPTION
See the documentation for BPpsilite.pm for a description of the Iteration.pm module.AUTHORS - Peter Schattner
Email: schattner@alum.mit.eduCONTRIBUTORS
Jason Stajich, jason@cgt.mc.duke.eduACKNOWLEDGEMENTS
Based on work of: Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf), Lorenz Pollak (lorenz@ist.org, bioperl port)COPYRIGHT
BPlite.pm is copyright (C) 1999 by Ian Korf.DISCLAIMER
This software is provided ``as is'' without warranty of any kind.query
Title : query Usage : $query = $obj->query(); Function : returns the query object Example : Returns : query object Args :
qlength
Title : qlength Usage : $len = $obj->qlength(); Returns : length of query Args : none
newhits
Title : newhits Usage : $newhits = $obj->newhits(); Returns : reference to an array listing all the hits from the current iteration which were not identified in the previous iteration Args : none
oldhits
Title : oldhits Usage : $oldhits = $obj->oldhits(); Returns : reference to an array listing all the hits from the current iteration which were identified and above threshold in the previous iteration Args : none
nextSbjct
Title : nextSbjct Usage : $sbjct = $obj->nextSbjct(); Function : Method of iterating through all the Sbjct retrieved from parsing the report #Example : while ( my $sbjct = $obj->nextSbjct ) {} Returns : next Sbjct object or undef if finished Args :
Align
Title : Align Usage : $SimpleAlign = $obj->Align(); Function : Method to obtain a simpleAlign object from psiblast Example : $SimpleAlign = $obj->Align(); Returns : SimpleAlign object or undef if not found. BUG : Only works if psiblast has been run with m 6 flag Args :
_readline
Title : _readline Usage : $obj->_readline Function: Reads a line of input. Note that this method implicitely uses the value of $/ that is in effect when called. Note also that the current implementation does not handle pushed back input correctly unless the pushed back input ends with the value of $/. Example : Returns :
_pushback
Title : _pushback Usage : $obj->_pushback($newvalue) Function: puts a line previously read with _readline back into a buffer Example : Returns : Args : newvalue
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre