Bio::SearchIO
hmmer_pull
Toolbar
Summary
Bio::SearchIO::hmmer_pull - A parser for HMMER output
Package variables
No package variables defined.
Inherit
Synopsis
# do not use this class directly it is available through Bio::SearchIO
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 't/data/hmmpfam.bigout');
while (my $result = $in->next_result) {
# this is a Bio::Search::Result::HmmpfamResult object
print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
while (my $hit = $result->next_hit) {
print $hit->name(), "\n";
while (my $hsp = $hit->next_hsp) {
print "length is ", $hsp->length(), "\n";
}
}
}
Description
This object implements a pull-parser for HMMER output. It is fast since it
only does work on request (hence 'pull').
Methods
Methods description
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none |
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed.
Returns : integer
Args : none |
Title : rewind
Usage : $searchio->rewind;
Function: Allow one to reset the Result iterator to the beginning, so that
next_result() will subsequently return the first result and so on.
NB: result objects are not cached, so you will get new result objects
each time you rewind. Also, note that result_count() counts the
number of times you have called next_result(), so will not be able
tell you how many results there were in the file if you use rewind().
Returns : n/a
Args : none |
Methods code
sub _initialize
{ my ($self, @args) = @_;
my ($writer, $file, $fh, $piped_behaviour, $evalue, $score, $hsps) =
$self->_rearrange([qw(WRITER
FILE FH
PIPED_BEHAVIOUR
EVALUE
SCORE
HSPS)], @args);
$self->writer($writer) if $writer;
$self->_fields( { ( header => undef,
algorithm => undef,
algorithm_version => undef,
algorithm_reference => '',
hmm_file => undef,
hmm_name => undef,
sequence_file => undef,
sequence_database => undef,
database_name => undef,
database_letters => undef,
database_entries => undef,
next_result => undef,
evalue_cutoff => '[unset]',
score_cutoff => '[unset]',
hsps_cutoff => '[unset]' ) } );
$self->_fields->{evalue_cutoff} = $evalue if $evalue;
$self->_fields->{score_cutoff} = $score if $score;
$self->_fields->{hsps_cutoff} = $hsps if $hsps;
$self->_dependencies( { ( algorithm => 'header',
algorithm_version => 'header',
hmm_file => 'header',
hmm_name => 'header',
sequence_file => 'header',
sequence_database => 'header' ) } );
$self->chunk($file || $fh || $self->throw("-file or -fh must be supplied"),
-piped_behaviour => $piped_behaviour || 'sequential_read');} | sub _discover_header
{ my $self = shift;
$self->_chunk_seek(0);
my $header = $self->_get_chunk_by_nol(8);
$self->{_after_header} = $self->_chunk_tell;
my ($algo) = $header =~ /^(hmm\S+) - search/m;
$self->_fields->{algorithm} = uc $algo;
($self->_fields->{algorithm_version}) = $header =~ /^HMMER\s+?(\S+)/m;
($self->_fields->{hmm_file}) = $header =~ /^HMM file:\s.+?(\S+)$/m;
$self->_fields->{hmm_name} = $self->_fields->{hmm_file};
($self->_fields->{sequence_file}) = $header =~ /^Sequence (?:file|database):\s.+?(\S+)$/m;
$self->_fields->{sequence_database} = $self->_fields->{sequence_file};
$self->_fields->{header} = 1;} | sub _discover_database_name
{ my $self = shift;
my $type = $self->get_field('algorithm');
if ($type eq 'HMMPFAM') {
$self->_fields->{database_name} = $self->get_field('hmm_file');
}
elsif ($type eq 'HMMSEARCH') {
$self->_fields->{database_name} = $self->get_field('sequence_file');
}} | sub _discover_next_result
{ my $self = shift;
my $type = $self->get_field('algorithm');
if ($type eq 'HMMPFAM') {
use Bio::Search::Result::HmmpfamResult;
unless ($self->_sequential) {
$self->_chunk_seek($self->{_end_of_previous_result} || $self->{_after_header});
my ($start, $end) = $self->_find_chunk_by_end("//\n");
return if $start == $end;
$self->_fields->{next_result} = Bio::Search::Result::HmmpfamResult->new(-chunk => [($self->chunk, $start, $end)],
-parent => $self);
$self->{_end_of_previous_result} = $end;
}
else {
my $chunk = $self->_get_chunk_by_end("//\n");
$chunk || return;
$self->_fields->{next_result} = Bio::Search::Result::HmmpfamResult->new(-chunk => [$chunk],
-parent => $self);
}
}
elsif ($type eq 'HMMSEARCH') {
$self->throw("Can't handle hmmsearch yet\n");
}
else {
$self->throw("Unknown report type");
}} | sub next_result
{ my $self = shift;
my $result = $self->get_field('next_result') || return;
undef $self->_fields->{next_result};
$self->{'_result_count'}++;
return $result;} | sub result_count
{ my $self = shift;
return $self->{'_result_count'};} | sub rewind
{ my $self = shift;
if ($self->_sequential) {
$self->warn("rewind has no effect on piped input when you have chosen 'sequential_read' mode");
}
delete $self->{_end_of_previous_result};
}
1;} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::SearchIO::hmmer_pull->new();
Function: Builds a new Bio::SearchIO::hmmer_pull object
Returns : Bio::SearchIO::hmmer_pull
Args : -fh/-file => HMMER output filename
-format => 'hmmer_pull'
-evalue => float or scientific notation number to be used
as an evalue cutoff for hits
-score => integer or scientific notation number to be used
as a score value cutoff for hits
-hsps => integer minimum number of hsps (domains) a hit must have
-piped_behaviour => 'temp_file'|'memory'|'sequential_read'
-piped_behaviour defines what the parser should do if the input is
an unseekable filehandle (eg. piped input), see
Bio::PullParserI::chunk for details. Default is 'sequential_read'.