Ewan Birney

NAME

Bio::Tools::BPbl2seq - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.

SYNOPSIS

  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->seqname;
         $hsp->sbjct->overlaps($exon);
 }

DESCRIPTION

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 the standard bioperl BLAST parsers Blast.pm and BPlite are 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.

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://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://bio.perl.org/bioperl-bugs/

AUTHOR - Peter Schattner

Email: schattner@alum.mit.edu

ACKNOWLEDGEMENTS

Based on work of: Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf), Lorenz Pollak (lorenz@ist.org, bioperl port)

CONTRIBUTORS

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

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