Bio::SearchIO megablast
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse
megablast reports (format 0)
Package variables
No package variables defined.
Inherit
Bio::SearchIO
Synopsis
# do not use this module directly
  use Bio::SearchIO;
# for default format output from megablast
my $in = Bio::SearchIO->new(-file => 'file.mbl',
-format => 'megablast',
-report_format => 0);
while( my $r = $in->next_result ) { while( my $hit = $r->next_hit ) { while( my $hsp = $hit->next_hsp ) { } } }
Description
Beware!
Because of the way megablast report format 0 is coded, realize that score
means # gap characters + # mismatches for a HSP.
The docs from NCBI regarding FORMAT 0
# 0: Produce one-line output for each alignment, in the form
#
# 'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score
#
# Here subject(query)-id is a gi number, an accession or some other type of
# identifier found in the FASTA definition line of the respective sequence.
#
# + or - corresponds to same or different strand alignment.
#
# Score for non-affine gapping parameters means the total number of
# differences (mismatches + gap characters). For affine case it is the
# actual (raw) score of the alignment.
FORMAT 1 parsing has not been implemented
FORMAT 2 parsing should work with the SearchIO 'blast' parser
Methods
BEGIN Code
_initialize
No description
Code
next_resultDescriptionCode
report_formatDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
charactersDescriptionCode
_modeDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
result_countDescriptionCode
Methods description
next_resultcode    nextTop
 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
report_formatcodeprevnextTop
 Title   : report_format
Usage : $obj->report_format($newval)
Function: Get/Set the report_format value
Returns : value of report_format (a scalar)
Args : on set, new value (a scalar or undef, optional)
start_elementcodeprevnextTop
 Title   : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
end_elementcodeprevnextTop
 Title   : start_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
elementcodeprevnextTop
 Title   : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
characterscodeprevnextTop
 Title   : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
_modecodeprevnextTop
 Title   : _mode
Usage : $obj->_mode($newval)
Function:
Example :
Returns : value of _mode
Args : newvalue (optional)
within_elementcodeprevnextTop
 Title   : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
in_elementcodeprevnextTop
 Title   : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
start_documentcodeprevnextTop
 Title   : start_document
Usage : $eventgenerator->start_document
Function: Handles a start document event
Returns : none
Args : none
end_documentcodeprevnextTop
 Title   : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
result_countcodeprevnextTop
 Title   : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
Methods code
BEGINTop
BEGIN {
    # mapping of MegaBlast terms to Bioperl hash keys
%MODEMAP = ('MegaBlastOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); # This should really be done more intelligently, like with
# XSLT
%MAPPING = ( 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hit_score' => 'HIT-score', 'Hsp_score' => 'HSP-score', 'Hsp_identity' => 'HSP-identical', 'Hsp_positive' => 'HSP-conserved', 'Hit_id' => 'HIT-name', 'MegaBlastOutput_program' => 'RESULT-algorithm_name', 'MegaBlastOutput_query-def'=> 'RESULT-query_name', ); $DEFAULT_BLAST_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter';
}
_initializedescriptionprevnextTop
sub _initialize {
    my ($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    my ($fmt) = $self->_rearrange([qw(REPORT_FORMAT)], @args);

    $self->throw("Must provide a value for -report_format when initializing a megablast parser") unless defined $fmt ;
    $self->report_format($fmt);
    return 1;
}
next_resultdescriptionprevnextTop
sub next_result {
   my ($self) = @_;
   
   local $/ = "\n";
   local $_;

   my $fmt = $self->report_format;
   my ($lastquery,$lasthit);
   while( defined($_ = $self->_readline) ) {
       if( $fmt == 0 ) {
	   if( /^\'(\S+)\'\=\=\'(\+|\-)(\S+)\'\s+
\((\d+)\s+(\d+)\s+(\d+)\s+(\d+)\)\s+
(\d+)/ox
) { my ($hit,$strand,$query, $h_start,$q_start,$h_end,$q_end, $score) = ($1,$2,$3,$4,$5,$6,$7,$8); if( ! defined $lastquery ) { $self->start_element({'Name' => 'MegaBlastOutput'}); $self->element({'Name' => 'MegaBlastOutput_program', 'Data' => 'MEGABLAST'}); $self->element({'Name' => 'MegaBlastOutput_query-def', 'Data' => $query}); } elsif( $lastquery ne $query ) { $self->_pushback($_); $self->end_element({'Name' => 'Hit'}) if( defined $lasthit); $self->end_element({ 'Name' => 'MegaBlastOutput'}); $lasthit = undef; $lastquery = undef; return $self->end_document(); } if( ! defined $lasthit || $lasthit ne $hit ) { $self->end_element({'Name' => 'Hit'}) if( defined $lasthit); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hit}); } $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_score', 'Data' => $score}); # flip flop start/end if strand is < 0
# since strandedness is inferred from the query
# because of the way it is coded all queries will
# be on the forward strand and hits will be either
# +/-
# also the NCBI docs state:
# 0: Produce one-line output for each alignment, in the form
#
# 'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score
#
# Here subject(query)-id is a gi number, an accession or some other type of
# identifier found in the FASTA definition line of the respective sequence.
#
# + or - corresponds to same or different strand alignment.
#
# Score for non-affine gapping parameters means the total number of
# differences (mismatches + gap characters). For affine case it is the
# actual (raw) score of the alignment.
# and yet when rev strand hits are made I see
# (MBL 2.2.4)
# 'Contig634'=='-503384' (1 7941 321 7620) 19
# so the query is on the rev strand and the
# subject is on the fwd strand
# so I am flip-flopping everything when I see a '-'
if( $strand eq '-' ) { ($h_start,$h_end) = ( $h_end,$h_start); ($q_start,$q_end) = ( $q_end,$q_start); } $self->element({'Name' => 'Hsp_hit-from', 'Data' => $h_start}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $h_end}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $q_start}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $q_end}); # might not be quite right -- need to know length of the HSP
my $numid = (abs($q_end - $q_start) - $score); $self->element({'Name' => 'Hsp_identity', 'Data' => $numid}); $self->element({'Name' => 'Hsp_positive', 'Data' => $numid}); $self->end_element({'Name' => 'Hsp'}); $lasthit = $hit; $lastquery = $query; } else { $self->debug("Unknown line in fmt0 parsing: $_"); } } } if( defined $lastquery && $fmt == 0 ) { $self->end_element({'Name' => 'Hit'}) if( defined $lasthit); $self->end_element({ 'Name' => 'MegaBlastOutput'}); return $self->end_document(); } return 0;
}
report_formatdescriptionprevnextTop
sub report_format {
    my $self = shift;
    return $self->{'_report_format'} = shift if @_;
    return $self->{'_report_format'};
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($self,$data) = @_;
    # we currently do not care about attributes
my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; } if($nm eq 'MegaBlastOutput') { $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $rc;

    if( my $type = $MODEMAP{$nm} ) {
	if( $self->_eventHandler->will_handle($type) ) {
	    my $func = sprintf("end_%s",lc $type);
	    $rc = $self->_eventHandler->$func($self->{'_reporttype'},
					      $self->{'_values'});
	}
	shift @{$self->{'_elements'}};

    } elsif( $MAPPING{$nm} ) {
	if ( ref($MAPPING{$nm}) =~ /hash/i ) {
	    my $key = (keys %{$MAPPING{$nm}})[0];
	    $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
	} else {
	    $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
	}
    } else {
	$self->warn( "unknown nm $nm ignoring\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if( $nm eq 'MegaBlastOutput' ); return $rc;
}
elementdescriptionprevnextTop
sub element {
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}
charactersdescriptionprevnextTop
sub characters {
   my ($self,$data) = @_;
   return unless defined $data->{'Data'};
   $self->{'_last_data'} = $data->{'Data'};
}
_modedescriptionprevnextTop
sub _mode {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_mode'} = $value;
    }
    return $self->{'_mode'};
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($self,$name) = @_;
   return 0 if ( ! defined $name &&
		 ! defined  $self->{'_elements'} ||
		 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       if( $_ eq $name  ) {
	   return 1;
       }
   }
   return 0;
}
in_elementdescriptionprevnextTop
sub in_element {
   my ($self,$name) = @_;
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_mode'} = '';
    $self->{'_elements'} = [];
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   return $self->{'_result'};
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $obj = Bio::SearchIO::blast->new();
Function: Builds a new Bio::SearchIO::blast object
Returns : Bio::SearchIO::blast
Args : -fh/-file => filehandle/filename to BLAST file
-format => 'blast'