NAME
Bio::Tools::BPlite - Lightweight BLAST parser
SYNOPSIS
use Bio::Tools::BPlite;
my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
{
$report->query;
$report->database;
while(my $sbjct = $report->nextSbjct) {
$sbjct->name;
while (my $hsp = $sbjct->nextHSP) {
$hsp->score;
$hsp->bits;
$hsp->percent;
$hsp->P;
$hsp->EXP;
$hsp->match;
$hsp->positive;
$hsp->length;
$hsp->querySeq;
$hsp->sbjctSeq;
$hsp->homologySeq;
$hsp->query->start;
$hsp->query->end;
$hsp->hit->start;
$hsp->hit->end;
$hsp->hit->seq_id;
$hsp->hit->overlaps($exon);
}
}
# the following line takes you to the next report in the stream/file
# it will return 0 if that report is empty,
# but that is valid for an empty blast report.
# Returns -1 for EOF.
last if ($report->_parseHeader == -1);
redo;
}DESCRIPTION
BPlite is a package for parsing BLAST reports. The BLAST programs are a family of widely used algorithms for sequence database searches. The reports are non-trivial to parse, and there are differences in the formats of the various flavors of BLAST. BPlite parses BLASTN, BLASTP, BLASTX, TBLASTN, and TBLASTX reports from both the high performance WU-BLAST, and the more generic NCBI-BLAST.
Many people have developed BLAST parsers (I myself have made at least three). BPlite is for those people who would rather not have a giant object specification, but rather a simple handle to a BLAST report that works well in pipes.
Object
BPlite has three kinds of objects, the report, the subject, and the HSP. To create a new report, you pass a filehandle reference to the BPlite constructor.
my $report = new Bio::Tools::BPlite(-fh=>\*STDIN); # or any other filehandleThe report has two attributes (query and database), and one method (nextSbjct).
$report->query; # access to the query name
$report->database; # access to the database name
$report->nextSbjct; # gets the next subject
while(my $sbjct = $report->nextSbjct) {
# canonical form of use is in a while loop
}A subject is a BLAST hit, which should not be confused with an HSP (below). A BLAST hit may have several alignments associated with it. A useful way of thinking about it is that a subject is a gene and HSPs are the exons. Subjects have one attribute (name) and one method (nextHSP).
$sbjct->name; # access to the subject name
$sbjct->nextHSP; # gets the next HSP from the sbjct
while(my $hsp = $sbjct->nextHSP) {
# canonical form is again a while loop
}An HSP is a high scoring pair, or simply an alignment. HSP objects inherit all the useful methods from RangeI/SeqFeatureI/FeaturePair, but provide an additional set of attributes (score, bits, percent, P, match, EXP, positive, length, querySeq, sbjctSeq, homologySeq) that should be familiar to anyone who has seen a blast report.
For lazy/efficient coders, two-letter abbreviations are available for the attributes with long names (qs, ss, hs). Ranges of the aligned sequences in query/subject and other information (like seqname) are stored in SeqFeature objects (i.e.: $hsp->query, $hsp->subject which is equal to $hsp->feature1, $hsp->feature2). querySeq, sbjctSeq and homologySeq do only contain the alignment sequences from the blast report.
$hsp->score;
$hsp->bits;
$hsp->percent;
$hsp->P;
$hsp->match;
$hsp->positive;
$hsp->length;
$hsp->querySeq; $hsp->qs;
$hsp->sbjctSeq; $hsp->ss;
$hsp->homologySeq; $hsp->hs;
$hsp->query->start;
$hsp->query->end;
$hsp->query->seq_id;
$hsp->hit->primary_tag; # "similarity"
$hsp->hit->source_tag; # "BLAST"
$hsp->hit->start;
$hsp->hit->end;
...So a very simple look into a BLAST report might look like this.
my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
while(my $sbjct = $report->nextSbjct) {
print ">",$sbjct->name,"\n";
while(my $hsp = $sbjct->nextHSP) {
print "\t",$hsp->start,"..",$hsp->end," ",$hsp->bits,"\n";
}
}The output of such code might look like this:
>foo
100..155 29.5
268..300 20.1
>bar
100..153 28.5
265..290 22.1AUTHORS
Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf), Lorenz Pollak (lorenz@ist.org, bioperl port)
ACKNOWLEDGEMENTS
This software was developed at the Genome Sequencing Center at Washington Univeristy, St. Louis, MO.
CONTRIBUTORS
Jason Stajich, jason@cgt.mc.duke.edu
COPYRIGHT
Copyright (C) 1999 Ian Korf. All Rights Reserved.
DISCLAIMER
This software is provided "as is" without warranty of any kind.
new
Title : new
Function: Create a new Bio::Tools::BPlite object
Returns : Bio::Tools::BPlite
Args : -file input file (alternative to -fh)
-fh input stream (alternative to -file)next_feature
Title : next_feature
Usage : while( my $feat = $res->next_feature ) { # do something }
Function: SeqAnalysisParserI implementing function. This implementation
iterates over all HSPs. If the HSPs of the current subject match
are exhausted, it will automatically call nextSbjct().
Example :
Returns : A Bio::SeqFeatureI compliant object, in this case a
Bio::Tools::BPlite::HSP object, and FALSE if there are no more
HSPs.
Args : Nonequery
Title : query
Usage : $query = $obj->query();
Function : returns the query object
Example :
Returns : query object
Args :qlength
Title : qlength
Usage : $len = $obj->qlength();
Function : returns the length of the query
Example :
Returns : length of query
Args :pattern
Title : pattern
Usage : $pattern = $obj->pattern();
Function : returns the pattern used in a PHIBLAST searchquery_pattern_location
Title : query_pattern_location
Usage : $qpl = $obj->query_pattern_location();
Function : returns reference to array of locations in the query sequence
of pattern used in a PHIBLAST searchdatabase
Title : database
Usage : $db = $obj->database();
Function : returns the database used in this search
Example :
Returns : database used for search
Args :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 null if finished
Args :