Bio::Tools::BPbl2seq - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm. use Bio::Tools::BPbl2seq; my $report = Bio::Tools::BPbl2seq->new(-file => 't/bl2seq.out'); $report->sbjctName; $report->sbjctLength; while(my $hsp = $report->next_feature) { $hsp->score; $hsp->bits; $hsp->percent; $hsp->P; $hsp->match; $hsp->positive; $hsp->length; $hsp->querySeq; $hsp->sbjctSeq; $hsp->homologySeq; $hsp->query->start; $hsp->query->end; $hsp->sbjct->start; $hsp->sbjct->end; $hsp->sbjct->seq_id; $hsp->sbjct->overlaps($exon); } BPbl2seq is a package for parsing BLAST bl2seq reports. BLAST bl2seq is a program for comparing and aligning two sequences using BLAST. Although the report format is similar to that of a conventional BLAST, there are a few differences so that BPlite is unable to read bl2seq reports directly. From the user's perspective, one difference between bl2seq and other blast reports is that the bl2seq report does not print out the name of the first of the two aligned sequences. (The second sequence name is given in the report as the name of the "hit"). Consequently, BPbl2seq has no way of identifying the name of the initial sequence unless it is passed to constructor as a second argument as in: my $report = Bio::Tools::BPbl2seq->new(\*FH, "ALEU_HORVU"); If the name of the first sequence (the "query") is not passed to BPbl2seq.pm in this manner, the name of the first sequence will be left as "unknown". (Note that to preserve a common interface with the other BLAST programs the two sequences being compared are referred to in bl2seq as "query" and "subject" although this is perhaps a bit misleading when simply comparing 2 sequences as opposed to querying a database.) In addition, since there will only be (at most) one "subject" (hit) in a bl2seq report, one should use the method $report->next_feature, rather than $report->nextSbjct->nextHSP to obtain the next high scoring pair. One should note that the previous (0.7) version of BPbl2seq used slightly different syntax. That version had a bug and consequently the old syntax has been eliminated. Attempts to use the old syntax will return error messages explaining the (minor) recoding required to use the current syntax.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: schattner@alum.mit.edu Based on work of: Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf), Lorenz Pollak (lorenz@ist.org, bioperl port) Jason Stajich, jason@cgt.mc.duke.edu

new
Title : new Function: Create a new Bio::Tools::BPbl2seq object Returns : Bio::Tools::BPbl2seq Args : -file input file (alternative to -fh) -fh input stream (alternative to -file) -queryname name of query sequence -report_type What type of BLAST was run (blastn,blastp,tblastn...)

getSbjct
Title : Usage : $sbjct = $obj->getSbjct(); Function : Method of obtaining single "subject" of a bl2seq report Example : my $sbjct = $obj->getSbjct ) {} Returns : Sbjct object or null if finished Args :

next_feature
Title : next_feature Usage : while( my $feat = $res->next_feature ) { # do something } Function: calls next_feature function from BPlite. 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 : None

queryName
Title : Usage : $name = $report->queryName(); Function : get /set the name of the query Example : Returns : name of the query Args :

sbjctName
Title : Usage : $name = $report->sbjctName(); Function : returns the name of the Sbjct Example : Returns : name of the Sbjct Args :

sbjctLength
Title : sbjctLength Usage : $length = $report->sbjctLength(); Function : returns the length of the Sbjct Example : Returns : name of the Sbjct Args :

P
Title : P Usage : Function : Syntax no longer supported, error message only

percent
Title : percent Usage : $hsp->percent(); Function : Syntax no longer supported, error message only

match
Title : match Usage : $hsp->match(); Function : Syntax no longer supported, error message only

positive
Title : positive Usage : $hsp->positive(); Function : Syntax no longer supported, error message only

querySeq
Title : querySeq Usage : $hsp->querySeq(); Function : Syntax no longer supported, error message only

sbjctSeq
Title : sbjctSeq Usage : $hsp->sbjctSeq(); Function : Syntax no longer supported, error message only

homologySeq
Title : homologySeq Usage : $hsp->homologySeq(); Function : Syntax no longer supported, error message only

qs
Title : qs Usage : $hsp->qs(); Function : Syntax no longer supported, error message only

ss
Title : ss Usage : $hsp->ss(); Function : Syntax no longer supported, error message only

hs
Title : hs Usage : $hsp->hs(); Function : Syntax no longer supported, error message only