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# $Id: blast_pull.pm 11480 2007-06-14 14:16:21Z sendu $
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# BioPerl module for Bio::SearchIO::blast_pull
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# Cared for by Sendu Bala <bix@sendu.me.uk>
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::SearchIO::blast_pull - A parser for BLAST output
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# do not use this class directly it is available through Bio::SearchIO
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my $in = Bio::SearchIO->new(-format => 'blast_pull',
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-file => 't/data/new_blastn.txt');
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while (my $result = $in->next_result) {
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# this is a Bio::Search::Result::BlastPullResult object
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print "Results for ", $result->query_name(), "\n";
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while (my $hit = $result->next_hit) {
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print $hit->name(), "\n";
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while (my $hsp = $hit->next_hsp) {
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print "length is ", $hsp->length(), "\n";
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This object implements a pull-parser for BLAST output. It is fast since it
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only does work on request (hence 'pull').
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Currently only NCBI BLASTN and BLASTP are supported.
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to
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the Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via the
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http://bugzilla.open-bio.org/
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=head1 AUTHOR - Sendu Bala
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The rest of the documentation details each of the object methods.
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Internal methods are usually preceded with a _
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# Let the code begin...
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package Bio::SearchIO::blast_pull;
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use Bio::Search::Result::BlastPullResult;
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use base qw(Bio::SearchIO Bio::PullParserI);
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Usage : my $obj = Bio::SearchIO::blast_pull->new();
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Function: Builds a new Bio::SearchIO::blast_pull object
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Returns : Bio::SearchIO::blast_pull
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Args : -fh/-file => BLAST output filename
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-format => 'blast_pull'
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-evalue => float or scientific notation number to be used
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as an evalue cutoff for hits
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-score => integer or scientific notation number to be used
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as a score value cutoff for hits
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-piped_behaviour => 'temp_file'|'memory'|'sequential_read'
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-piped_behaviour defines what the parser should do if the input is
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an unseekable filehandle (eg. piped input), see
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Bio::PullParserI::chunk for details. Default is 'memory'.
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my ($self, @args) = @_;
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# don't do normal SearchIO initialization
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my ($writer, $file, $fh, $piped_behaviour, $evalue, $score) =
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$self->_rearrange([qw(WRITER
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$self->writer($writer) if $writer;
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$self->_fields( { ( header => undef,
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algorithm_version => undef,
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algorithm_reference => '',
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database_name => undef,
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database_letters => undef,
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database_entries => undef,
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next_result => undef,
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evalue_cutoff => '[unset]',
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score_cutoff => '[unset]' ) } );
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$self->_fields->{evalue_cutoff} = $evalue if $evalue;
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$self->_fields->{score_cutoff} = $score if $score;
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$self->_dependencies( { ( algorithm => 'header',
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algorithm_version => 'header',
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database_name => 'header',
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database_letters => 'header',
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database_entries => 'header' ) } );
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$self->chunk($file || $fh || $self->throw("-file or -fh must be supplied"),
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-piped_behaviour => $piped_behaviour || 'memory');
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sub _discover_header {
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$self->_chunk_seek(0);
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my $header = $self->_get_chunk_by_end("\nQuery=");
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$self->{_after_header} = $self->_chunk_tell;
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#*** won't catch all types? only support blastn/p now anyway
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$header =~ /^(\S+) (\S+\s+\S+)/;
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$self->_fields->{algorithm} = $1;
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$self->_fields->{algorithm_version} = $2;
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my ($database) = $header =~ /^Database: (.+)/sm;
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# earlier versions put query before database?
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my $header2 = $self->_get_chunk_by_end(".done\n");
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($database) = $header2 =~ /^Database: (.+)/sm;
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$database =~ s/\s+(\d\S+) sequences; (\d\S+) total letters.*//s;
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$database =~ s/\n//g;
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$self->_fields->{database_name} = $database;
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$self->_fields->{database_entries} = $entries;
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$self->_fields->{database_letters} = $letters;
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$self->_fields->{header} = 1;
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sub _discover_next_result {
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return if $self->{_after_results};
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my $type = $self->get_field('algorithm'); # also sets _after_header if not set
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if ($type eq 'BLASTN' || $type eq 'BLASTP') {
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unless ($self->_sequential) {
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$self->_chunk_seek($self->{_end_of_previous_result} || $self->{_after_header});
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my ($start, $end) = $self->_find_chunk_by_end("\nQuery=");
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return if ($start == $end);
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$start = $self->{_end_of_previous_result} || $self->{_after_header};
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$self->_fields->{next_result} = Bio::Search::Result::BlastPullResult->new(-chunk => [($self->chunk, $start, $end)],
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$self->{_end_of_previous_result} = $end;
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#*** doesn't work for the last result, needs fixing - try getting the database end chunk on failure?...
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$self->throw("sequential mode not yet implemented");
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my $chunk = $self->_get_chunk_by_end("\nQuery=");
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$self->_fields->{next_result} = Bio::Search::Result::BlastPullResult->new(-chunk => [$chunk],
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$self->throw("Can only handle NCBI BLASTN and BLASTP right now");
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Usage : my $hit = $searchio->next_result;
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Function: Returns the next Result from a search
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Returns : Bio::Search::Result::ResultI object
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my $result = $self->get_field('next_result') || return;
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undef $self->_fields->{next_result};
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$self->{'_result_count'}++;
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Usage : my $count = $searchio->result_count
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Function: Returns the number of results we have processed.
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return $self->{'_result_count'};
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Usage : $searchio->rewind;
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Function: Allow one to reset the Result iterator to the beginning, so that
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next_result() will subsequently return the first result and so on.
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NB: result objects are not cached, so you will get new result objects
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each time you rewind. Also, note that result_count() counts the
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number of times you have called next_result(), so will not be able
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tell you how many results there were in the file if you use rewind().
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delete $self->{_end_of_previous_result};
added
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Bio/SearchIO/blast_pull.pm
