Bio::SearchIO fasta
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Summary
Bio::SearchIO::fasta - A SearchIO parser for FASTA results
Package variables
No package variables defined.
Included modules
Bio::Factory::ObjectFactory
Inherit
Bio::SearchIO
Synopsis
  # Do not use this object directly, use it through the SearchIO system
use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-format => 'fasta',
-file => 'report.FASTA');
while( my $result = $searchio->next_result ) {
# ... do what you would normally doi with Bio::SearchIO.
}
Description
This object contains the event based parsing code for FASTA format
reports. It creates Bio::Search::HSP::FastaHSP objects instead of
Bio::Search::HSP::GenericHSP for the HSP objects.
This module will parse -m 9 -d 0 output as well as default m 1 output
from FASTA as well as SSEARCH.
Also see the SearchIO HOWTO:
http://bioperl.open-bio.org/wiki/HOWTO:SearchIO.
Methods
BEGIN Code
_initialize
No description
Code
next_resultDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
charactersDescriptionCode
_modeDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
idlengthDescriptionCode
result_countDescriptionCode
attach_EventHandler
No description
Code
_will_handleDescriptionCode
_processHitsDescriptionCode
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
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
idlengthcodeprevnextTop
 Title   : idlength
Usage : $obj->idlength($newval)
Function: Internal storage of the length of the ID desc
in the HSP alignment blocks. Defaults to
$IDLENGTH class variable value
Returns : value of idlength
Args : newvalue (optional)
result_countcodeprevnextTop
 Title   : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
_will_handlecodeprevnextTop
 Title   : _will_handle
Usage : Private method. For internal use only.
if( $self->_will_handle($type) ) { ... }
Function: Provides an optimized way to check whether or not an element of a
given type is to be handled.
Returns : Reference to EventHandler object if the element type is to be handled.
undef if the element type is not to be handled.
Args : string containing type of element.
Optimizations:
  1
  Using the cached pointer to the EventHandler to minimize repeated
lookups.
  2
  Caching the will_handle status for each type that is encountered so
that it only need be checked by calling
handler->will_handle($type) once.
This does not lead to a major savings by itself (only 5-10%). In
combination with other optimizations, or for large parse jobs, the
savings good be significant.
To test against the unoptimized version, remove the parentheses from
around the third term in the ternary " ? : " operator and add two
calls to $self->_eventHandler().
_processHitscodeprevnextTop
 Title   : _processHits
Usage : Private method. For internal use only.
Function: Process/report any hits/hsps we saw in the top table, not in alignments.
Returns : nothing.
Args : array of hits to process.
Methods code
BEGINTop
BEGIN {
    # Set IDLENGTH to a new value if you have
# compile FASTA with a different ID length
# (actually newest FASTA allows the setting of this
# via -C parameter, default is 6)
$IDLENGTH = 6; # mapping of NCBI Blast terms to Bioperl hash keys
%MODEMAP = ( 'FastaOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); # This should really be done more intelligently, like with
# XSLT
%MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_sw-score' => 'HSP-swscore', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_evalue2' => 'HSP-evalue2', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame' => 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'FastaOutput_program' => 'RESULT-algorithm_name', 'FastaOutput_version' => 'RESULT-algorithm_version', 'FastaOutput_query-def' => 'RESULT-query_name', 'FastaOutput_querydesc' => 'RESULT-query_description', 'FastaOutput_query-len' => 'RESULT-query_length', 'FastaOutput_db' => 'RESULT-database_name', 'FastaOutput_db-len' => 'RESULT-database_entries', 'FastaOutput_db-let' => 'RESULT-database_letters', 'Parameters_matrix' => { 'RESULT-parameters' => 'matrix' }, 'Parameters_expect' => { 'RESULT-parameters' => 'expect' }, 'Parameters_include' => { 'RESULT-parameters' => 'include' }, 'Parameters_sc-match' => { 'RESULT-parameters' => 'match' }, 'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch' }, 'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen' }, 'Parameters_gap-ext' => { 'RESULT-parameters' => 'gapext' }, 'Parameters_word-size' => { 'RESULT-parameters' => 'wordsize' }, 'Parameters_ktup' => { 'RESULT-parameters' => 'ktup' }, 'Parameters_filter' => { 'RESULT-parameters' => 'filter' }, 'Statistics_db-num' => { 'RESULT-statistics' => 'dbentries' }, 'Statistics_db-len' => { 'RESULT-statistics' => 'dbletters' }, 'Statistics_hsp-len' => { 'RESULT-statistics' => 'hsplength' }, 'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace' }, 'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' }, 'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' }, 'Statistics_entropy' => { 'RESULT-statistics' => 'entropy' }, );
}
_initializedescriptionprevnextTop
sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    return unless @args;
    my ($idlength) = $self->_rearrange( [qw(IDLENGTH)], @args );
    $self->idlength( $idlength || $IDLENGTH );
    $self->_eventHandler->register_factory(
        'hsp',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::HSP::FastaHSP',
            -interface => 'Bio::Search::HSP::HSPI'
        )
    );
    return 1;
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    local $/ = "\n";
    local $_;

    my $data    = '';
    my $seentop = 0;
    my $current_hsp;
    my $m9HSP = 0;
    $self->start_document();
    my @hit_signifs;
    while ( defined( $_ = $self->_readline ) ) {
        next if ( !$self->in_element('hsp')
            && /^\s+$/ );    # skip empty lines
if ( m/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/oxi
|| /(\S+)\s+compares\s+a/
|| /(\S+)\s+performs\s+a/
|| /(\S+)\s+produces\s/
|| /(\S+)\s+finds\s+/ # for lalign, but does not work because no "The best scores are:"
|| ( m/^\#\s+/ # has a command log line
&& (
$_ = $self->_readline )
&& /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/oxi
|| /(\S+)\s+compares\s+a/
|| /(\S+)\s+performs\s+a/
|| /(\S+)\s+produces\s/
|| /(\S+)\s+finds\s+/ # for lalign, but does not work because no "The best scores are:"
)
)
{
if (
$seentop) {
$self->_pushback($_);
$self->end_element( { 'Name' => 'FastaOutput' } ); return $self->end_document(); } $self->{'_reporttype'} = $1; $self->start_element( { 'Name' => 'FastaOutput' } ); $self->{'_result_count'}++; $seentop = 1; #$self->debug( "reporttype is " . $self->{'_reporttype'} . "\n" );
$self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); my $version; # version 35 version string on same line
if (/version/) { ($version) = (/version\s+(\S+)/); } # earlier versions, it's on the next line
else { $_ = $self->_readline(); ($version) = (/version\s+(\S+)/); } $version = '' unless defined $version; $self->{'_version'} = $version; $self->element( { 'Name' => 'FastaOutput_version', 'Data' => $version } ); my ( $last, $leadin, $type, $querylen, $querytype, $querydef ); while ( defined( $_ = $self->_readline() ) ) { if ( /^ (
(?:\s+>) | # fa33 lead-in
(?:\s*\d+\s*>>>) # fa34 mlib lead-in
)
(.*)
/x
) { ( $leadin, $querydef ) = ( $1, $2 ); if ( $leadin =~ m/>>>/ ) {
if (
$querydef =~
/^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o )
{
( $querydef, $querylen, $querytype ) =
( $1, $2, $3 );
last; } } else { if ( $last =~ /(\S+)[:,]\s*(\d+)\s+(aa|nt)/ ) { ( $querylen, $querytype ) = ( $2, $3 ); $querydef ||= $1; last; } } } elsif (m/^\s*vs\s+\S+/o) {
if (
$last =~ /(\S+)[,:]\s+(\d+)\s+(aa|nt)/o ) {
(
$querydef, $querylen, $querytype ) = ( $1, $2, $3 );
last; } } $last = $_; } if ( $self->{'_reporttype'} && $self->{'_reporttype'} eq 'FASTA' ) { if ( $querytype eq 'nt' ) { $self->{'_reporttype'} = 'FASTN'; } elsif ( $querytype eq 'aa' ) { $self->{'_reporttype'} = 'FASTP'; } } my ( $name, $descr ) = $querydef =~ m/^(\S+)\s*(.*?)\s*$/o;
$self->element( { 'Name' => 'FastaOutput_query-def', 'Data' => $name } ); $self->element( { 'Name' => 'FastaOutput_querydesc', 'Data' => $descr } ); if ($querylen) { $self->element( { 'Name' => 'FastaOutput_query-len', 'Data' => $querylen } ); } else { $self->warn("unable to find and set query length"); } if ( $last =~ /^\s*vs\s+(\S+)/ || ( $last =~ /^searching\s+(\S+)\s+library/ ) || ( $last =~ /^Library:\s+(\S+)\s+/ ) || ( defined $_ && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)\s+/ ) ) || ( defined( $_ = $self->_readline() ) && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ ) ) ) { $self->element( { 'Name' => 'FastaOutput_db', 'Data' => $1 } ); } elsif (m/^\s+opt(?:\s+E\(\))?$/o) {

# histogram ... read over it more rapidly than the larger outer loop:
while ( defined( $_ = $self->_readline ) ) {
last if m/^>\d+/;
} } } elsif (/(\d+)\s+residues\s+in\s+(\d+)\s+(?:library\s+)?sequences/) { $self->element( { 'Name' => 'FastaOutput_db-let', 'Data' => $1 } ); $self->element( { 'Name' => 'FastaOutput_db-len', 'Data' => $2 } ); $self->element( { 'Name' => 'Statistics_db-len', 'Data' => $1 } ); $self->element( { 'Name' => 'Statistics_db-num', 'Data' => $2 } ); } elsif (/Lambda=\s*(\S+)/) { $self->element( { 'Name' => 'Statistics_lambda', 'Data' => $1 } ); } elsif (/K=\s*(\S+)/) { $self->element( { 'Name' => 'Statistics_kappa', 'Data' => $1 } ); } elsif (/^\s*(Smith-Waterman)/) { $self->{'_reporttype'} = $1; m/\[\s*(\S+)\s+matrix \([^\)]+\)(xS)?\],/;
$self->element( { 'Name' => 'Parameters_matrix', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_filter', 'Data' => defined $2 ? 1 : 0, } ); if (/\s*gap\-penalty:\s*(\-?\d+)\/(\-?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1, } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2, } ); } elsif (/\s*open\/ext:\s*(\-?\d+)\/(\-?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1, } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2, } ); } $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); } elsif (/The best( related| unrelated)? scores are:/) { my $rel = $1; my @labels = split; @labels = map { if ( $_ =~ m/^E\((\d+)\)$/o )
{
$self->element(
{ 'Name' => 'Statistics_eff-space', 'Data' => $1 } );
"evalue"; } else { # canonicalize changed column headers
if ($_ eq "gapl") { $_ = "lgaps"; } elsif ($_ eq "gapq") { $_ = "qgaps"; } elsif ($_ eq "E2()") { $_ = "evalue2"; } $_; } } @labels[ $rel ? 5 : 4 .. $#labels ]; while ( defined( $_ = $self->_readline() ) && !/^\s+$/ ) { my @line = split; if ( $line[-1] =~ m/\=/o && $labels[-1] ne 'aln_code' ) {
# unlabelled alignment hit;
push @labels, "aln_code"; } if ($line[0] eq "+-") { $m9HSP = 1; # parse HSP, add to last parsed Hit
my %hspData; my @line = split; @hspData{@labels} = splice( @line, @line - @labels ); $hspData{lframe} = $hit_signifs[-1]->{lframe}; push @{$hit_signifs[-1]->{HSPs}},\% hspData; next; } elsif ($line[0] eq '>>><<<') { last; } my (%data, %hspData); @data{@labels} = @hspData{@labels} = splice( @line, @line - @labels ); if ( $line[-1] =~ m/\[([1-6rf])\]/o ) {
my
$fr = $1;
$hspData{lframe} = $data{lframe} = ( $fr =~ /\d/o ? ( $fr <= 3 ? "+$fr" : "-@{[$fr-3]}" ) : ( $fr eq 'f' ? '+1' : '-1' ) ); pop @line; } else { $hspData{lframe} = $data{lframe} = '0'; } if ( $line[-1] =~ m/^\(?(\d+)\)$/ ) {
$data{hit_len} = $1;
pop @line; if ( $line[-1] =~ m/^\($/ ) {
pop @line;
} } else { $data{hit_len} = 0; } # rebuild the first part of the line, preserving spaces:
($_) = m/^(\S+(?:\s+\S+){$#line})/;
my ( $id, $desc ) = split( /\s+/, $_, 2 ); my @pieces = split( /\|/, $id ); my $acc = pop @pieces; $acc =~ s/\.\d+$//; @data{qw(id desc acc)} = ( $id, $desc, $acc ); $data{HSPs} = [\% hspData ]; push @hit_signifs,\% data; } } elsif ( /^\s*([T]?FAST[XYAF]).+,\s*(\S+)\s*matrix[^\]]+?(xS)?\]\s*ktup:\s*(\d+)/ ) { $self->element( { 'Name' => 'Parameters_matrix', 'Data' => $2 } ); $self->element( { 'Name' => 'Parameters_filter', 'Data' => defined $3 ? 1 : 0, } ); $self->element( { 'Name' => 'Parameters_ktup', 'Data' => $4 } ); $self->{'_reporttype'} = $1 if ( $self->{'_reporttype'} !~ /FAST[PN]/i ); #
# get gap-pen line for FASTA33, which is not on the matrix line
#
# FASTA (3.36 June 2000) function [optimized, BL50 matrix (15:-5)] ktup: 2
# join: 36, opt: 24, gap-pen: -12/ -2, width: 16
#
$_ = $self->_readline(); if (/(?:gap\-pen|open\/ext):\s+([\-\+]?\d+)\s*\/\s*([\-\+]?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2 } ); } $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); } elsif (/^Algorithm:\s+(\S+)\s+.*\s*\(([^)]+)\)\s+(\S+)/) { $self->{'_reporttype'} = $1 if ( $self->{'_reporttype'} !~ /FAST[PN]/i ); } elsif ( /^Parameters:/ ) { # FASTA 35.04/FASTA 36
m/Parameters:\s+(\S+)\s+matrix\s+\([^\)]+\)(xS)?,?\s/;
$self->element( { 'Name' => 'Parameters_matrix', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_filter', 'Data' => defined $2 ? $2 : 0, } ); if (/ktup:\s(\d+)/) { $self->element( { 'Name' => 'Parameters_ktup', 'Data' => $1 } ); if (/ktup:\s\d+$/) { $_ = $self->_readline(); } } if (/(?:gap\-pen|open\/ext):\s+([\-\+]?\d+)\s*\/\s*([\-\+]?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2 } ); } $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); } elsif ( /^\s+ktup:\s*(\d+),/ ) { $self->element( { 'Name' => 'Parameters_ktup', 'Data' => $1 } ); } elsif (/^(>--)$/ || /^>>(?!>)(.+?)\s+(?:\((\d+)\s*(aa|nt)\))?$/) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } my $firstHSP = 0; if ($1 ne ">--") { $firstHSP = 1; my ($hit_id, $len, $alphabet) = ($1, $2, $3); if (!$len || !$alphabet) { WRAPPED: while (defined($_ = $self->_readline)) { if (/(.*?)\s+\((\d+)\s*(aa|nt)\)/) { ($len, $alphabet) = ($2, $3); $hit_id .= $1 ? " ".$1 : ''; last WRAPPED; } if (/^>>(?!>)/) { # too far, throw
$self->throw("Couldn't find length, bailing"); } } } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_len', 'Data' => $len } ); my ( $id, $desc ) = split( /\s+/, $hit_id, 2 ); $self->element( { 'Name' => 'Hit_id', 'Data' => $id } ); #$self->debug("Hit ID is $id\n");
my @pieces = split( /\|/, $id ); my $acc = pop @pieces; $acc =~ s/\.\d+$//; $self->element( { 'Name' => 'Hit_accession', 'Data' => $acc } ); $self->element( { 'Name' => 'Hit_def', 'Data' => $desc } ); } else { # push @{$hit_signifs[0]->{HSPs}}, $current_hsp;
} $_ = $self->_readline(); my ( $score, $bits, $e, $e2 ) = /Z-score: \s* (\S+) \s*
(?: bits: \s* (\S+) \s+ )?
(?: E|expect ) \s* \((?:\d+)?\) :? \s*(\S+)
(?: \s* E2 \s* \(\) :? \s*(\S+) )?
/ox
; $bits = $score unless defined $bits; my ($v); if ($firstHSP && !$m9HSP) { $v = shift @{$hit_signifs[0]->{HSPs}} if (@hit_signifs && @{$hit_signifs[0]->{HSPs}}); $current_hsp = $v; } else { $v = $current_hsp; } if ( defined $v ) { @{$v}{qw(evalue evalue2 bits z-sc)} = ( $e, $e2, $bits, $score ); } if ($firstHSP) { $self->element( { 'Name' => 'Hit_signif', 'Data' => $v ? $v->{evalue} : $e } ); $self->element( { 'Name' => 'Hit_score', 'Data' => $v ? $v->{bits} : $bits } ); } $self->start_element( { 'Name' => 'Hsp' } ); $self->element( { 'Name' => 'Hsp_score', 'Data' => $v ? $v->{'z-sc'} : $score } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $v ? $v->{evalue} : $e } ); $self->element( { 'Name' => 'Hsp_evalue2', 'Data' => $v && exists($v->{evalue2}) ? $v->{evalue2} : $e2 } ) if (($v && exists($v->{evalue2})) || defined $e2); $self->element( { 'Name' => 'Hsp_bit-score', 'Data' => $v ? $v->{bits} : $bits } ); $_ = $self->_readline(); if (s/global\/.* score:\s*(\d+)\;?//) { $self->element( { 'Name' => 'Hsp_sw-score', 'Data' => $1 } ); } if (s/Smith-Waterman score:\s*(\d+)\;?//) { $self->element( { 'Name' => 'Hsp_sw-score', 'Data' => $1 } ); } if ( / (\d*\.?\d+)\% \s* identity
(?:\s* \(\s*(\S+)\% \s* (?:ungapped|similar) \) )?
\s* in \s* (\d+) \s+ (?:aa|nt) \s+ overlap \s*
\( (\d+) \- (\d+) : (\d+) \- (\d+) \)
/x
) { my ( $identper, $gapper, $len, $querystart, $queryend, $hitstart, $hitend ) = ( $1, $2, $3, $4, $5, $6, $7 ); my $ident = sprintf( "%.0f", ( $identper / 100 ) * $len );
my $positive = sprintf( "%.0f", ( $gapper / 100 ) * $len );
$self->element( { 'Name' => 'Hsp_identity', 'Data' => $ident } ); $self->element( { 'Name' => 'Hsp_positive', 'Data' => $positive } ); $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $len } ); $self->element( { 'Name' => 'Hsp_query-from', 'Data' => $querystart } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => $queryend } ); $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => $hitstart } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => $hitend } ); } if ($v) { $self->element( { 'Name' => 'Hsp_querygaps', 'Data' => $v->{qgaps} } ) if exists $v->{qgaps}; $self->element( { 'Name' => 'Hsp_hitgaps', 'Data' => $v->{lgaps} } ) if exists $v->{lgaps}; if ( $self->{'_reporttype'} =~ m/^FAST[NXY]$/o ) {
if ( 8 == scalar grep { exists $v->{$_} }
qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) )
{
if ( $v->{ax0} < $v->{an0} ) {
$self->element(
{
'Name' => 'Hsp_query-frame',
'Data' =>
"-@{[(($v->{px0} - $v->{ax0}) % 3) + 1]}"
}
);
} else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => "+@{[(($v->{an0} - $v->{pn0}) % 3) + 1]}" } ); } if ( $v->{ax1} < $v->{an1} ) { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "-@{[(($v->{px1} - $v->{ax1}) % 3) + 1]}" } ); } else { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "+@{[(($v->{an1} - $v->{pn1}) % 3) + 1]}" } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => $v->{lframe} } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => 0 } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => 0 } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => $v->{lframe} } ); } } else { $self->warn("unable to parse FASTA score line: $_"); } } elsif (/\d+\s*residues\s*in\s*\d+\s*query\s*sequences/) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } # $_ = $self->_readline();
# my ( $liblen,$libsize) = /(\d+)\s+residues\s*in(\d+)\s*library/;
# fast forward to the end of the file as there is
# nothing else left to do with this file and want to be sure and
# reset it
while ( defined( $_ = $self->_readline() ) ) { last if (/^Function used was/); if ( /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?
sequence/oxi
|| /(\S+)\s+compares\s+a/oi ) { $self->_pushback($_); } } $self->_processHits(@hit_signifs) if @hit_signifs; $self->end_element( { 'Name' => 'FastaOutput' } ); return $self->end_document(); } elsif (/^\s*\d+\s*>>>/) { if ( $self->within_element('FastaOutput') ) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } $self->_processHits(@hit_signifs) if (@hit_signifs); $self->end_element( { 'Name' => 'FastaOutput' } ); $self->_pushback($_); return $self->end_document(); } else { $self->start_element( { 'Name' => 'FastaOutput' } ); $self->{'_result_count'}++; $seentop = 1; $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); $self->element( { 'Name' => 'FastaOutput_version', 'Data' => $self->{'_version'} } ); my ( $type, $querylen, $querytype, $querydef ); if (/^\s*\d+\s*>>>(.*)/) { $querydef = $1; if ( $querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o ) { ( $querydef, $querylen, $querytype ) = ( $1, $2, $3 ); } } if ( $self->{'_reporttype'} && $self->{'_reporttype'} eq 'FASTA' ) { if ( $querytype eq 'nt' ) { $self->{'_reporttype'} = 'FASTN'; } elsif ( $querytype eq 'aa' ) { $self->{'_reporttype'} = 'FASTP'; } } my ( $name, $descr ) = ( $querydef =~ m/^(\S+)(?:\s+(.*))?\s*$/o );
$self->element( { 'Name' => 'FastaOutput_query-def', 'Data' => $name } ); $self->element( { 'Name' => 'FastaOutput_querydesc', 'Data' => $descr } ); if ($querylen) { $self->element( { 'Name' => 'FastaOutput_query-len', 'Data' => $querylen } ); } else { $self->warn("unable to find and set query length"); } if ( defined( $_ = $self->_readline() ) && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ ) ) { $self->element( { 'Name' => 'FastaOutput_db', 'Data' => $1 } ); } } } elsif ( $self->in_element('hsp') ) { my @data = ( [], [], [] ); my $count = 0; my $len = $self->idlength + 1; my ($seq1_id); while ( defined($_) ) { chomp; #$self->debug("$count $_\n");
if (/residues in \d+\s+query\s+sequences/o) { $self->_pushback($_); last; } elsif (/^>>>\*\*\*/o) { $self->end_element( { Name => "Hsp" } ); last; } elsif (/^>>/o) { $self->_pushback($_); last; } elsif (/^\s*\d+\s*>>>/o) { $self->_pushback($_); last; } if ( $count == 0 ) { if (/^(\S+)\s+/) { $self->_pushback($_); $count = 2; } elsif ( /^\s+\d+/ || /^\s+$/ ) { # do nothing, this is really a 0 line
} elsif ( length($_) == 0 ) { $count = -1; } else { $self->_pushback($_); $count = 0; } } elsif ( $count == 1 || $count == 3 ) { if (/^(\S+)\s+/) { $len = CORE::length($1) if $len < CORE::length($1); s/\s+$//; # trim trailing spaces,we don't want them
push @{ $data[ $count - 1 ] }, substr( $_, $len ); } elsif (/^\s+(\d+)/) { $count = -1; $self->_pushback($_); } elsif ( /^\s+$/ || length($_) == 0 ) { $count = 5; # going to skip these
} elsif ( /\s+\S+fasta3\d\s+/) { # this is something that looks like a path but contains
# the fasta3x executable string, such as:
# /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i test.fa ../other_mirs.fa -O test.fasta35
last; } else { $self->throw( "Unrecognized alignment line ($count) '$_'"); } } elsif ( $count == 2 ) { if (/^\s+\d+\s+/) { $self->warn("$_\n") if $self->verbose > 0; # we are on a Subject part of the alignment
# but we THOUGHT we were on the Query
# move that last line to the proper place
push @{ $data[2] }, pop @{ $data[0] }; $count = 4; } else { # toss the first IDLENGTH characters of the line
if ( length($_) >= $len ) { push @{ $data[ $count - 1 ] }, substr( $_, $len ); } } } last if ( $count++ >= 5 ); $_ = $self->_readline(); } if ( @{ $data[0] } || @{ $data[2] } ) { $self->characters( { 'Name' => 'Hsp_qseq', 'Data' => join( '', @{ $data[0] } ) } ); $self->characters( { 'Name' => 'Hsp_midline', 'Data' => join( '', @{ $data[1] } ) } ); $self->characters( { 'Name' => 'Hsp_hseq', 'Data' => join( '', @{ $data[2] } ) } ); } } else { if ( !$seentop ) { $self->debug($_); #$self->warn("unrecognized FASTA Family report file!");
#return;
} } } if ( $self->in_element('result') ) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } $self->end_element( { 'Name' => 'FastaOutput' } ); } return $self->end_document();
}
start_elementdescriptionprevnextTop
sub start_element {
    my ( $self, $data ) = @_;

    # we currently don't care about attributes
my $nm = $data->{'Name'}; if ( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if ( my $handler = $self->_will_handle($type) ) { my $func = sprintf( "start_%s", lc $type ); $handler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( $nm eq 'FastaOutput' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_mode'} = ''; }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ( $self, $data ) = @_;
    my $nm = $data->{'Name'};
    my $rc;

    # Hsp are sort of weird, in that they end when another
# object begins so have to detect this in end_element for now
if ( $nm eq 'Hsp' ) { foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq)) { $self->element( { 'Name' => $_, 'Data' => $self->{'_last_hspdata'}->{$_} } ); } $self->{'_last_hspdata'} = {}; } if ( my $type = $MODEMAP{$nm} ) { if ( my $handler = $self->_will_handle($type) ) { my $func = sprintf( "end_%s", lc $type ); $rc = $handler->$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 'FastaOutput' ); 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'} );
    if ( $data->{'Data'} =~ /^\s+$/ ) {
        return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/;
    }

    if (   $self->in_element('hsp')
        && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ )
    {

        $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $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 || $_ eq $MODEMAP{$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
          || ( exists $MODEMAP{$name}
            && $self->{'_elements'}->[0] eq $MODEMAP{$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'};
}
idlengthdescriptionprevnextTop
sub idlength {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_idlength'} = $value;
    }
    return $self->{'_idlength'} || $IDLENGTH;
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
attach_EventHandlerdescriptionprevnextTop
sub attach_EventHandler {
    my ( $self, $handler ) = @_;

    $self->SUPER::attach_EventHandler($handler);

    # Optimization: caching the EventHandler since it is used a lot
# during the parse.
$self->{'_handler_cache'} = $handler; return;
}
_will_handledescriptionprevnextTop
sub _will_handle {
    my ( $self, $type ) = @_;
    my $handler = $self->{'_handler_cache'};
    my $will_handle =
      defined( $self->{'_will_handle_cache'}->{$type} )
      ? $self->{'_will_handle_cache'}->{$type}
      : ( $self->{'_will_handle_cache'}->{$type} =
          $handler->will_handle($type) );

    return $will_handle ? $handler : undef;
}
_processHitsdescriptionprevnextTop
sub _processHits {
  my ($self, @hit_signifs) = @_;

  # process remaining best hits
for my $hit (@hit_signifs) { # Hsp_score Hsp_evalue Hsp_bit-score
# Hsp_sw-score Hsp_gaps Hsp_identity Hsp_positive
# Hsp_align-len Hsp_query-from Hsp_query-to
# Hsp_hit-from Hsp_hit-to Hsp_qseq Hsp_midline
$self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_len', 'Data' => $hit->{hit_len} } ) if exists $hit->{hit_len}; $self->element( { 'Name' => 'Hit_id', 'Data' => $hit->{id} } ) if exists $hit->{id}; $self->element( { 'Name' => 'Hit_accession', 'Data' => $hit->{acc} } ) if exists $hit->{acc}; $self->element( { 'Name' => 'Hit_def', 'Data' => $hit->{desc} } ) if exists $hit->{desc}; $self->element( { 'Name' => 'Hit_signif', 'Data' => $hit->{evalue} } ) if exists $hit->{evalue}; $self->element( { 'Name' => 'Hit_score', 'Data' => $hit->{bits} } ) if exists $hit->{bits}; for my $hsp (@{$hit->{HSPs}}) { $self->start_element( { 'Name' => 'Hsp' } ); $self->element({'Name' => 'Hsp_score', 'Data' => $hsp->{'z-sc'}}) if exists $hsp->{'z-sc'}; $self->element({'Name' => 'Hsp_evalue', 'Data' => $hsp->{evalue} } ) if exists $hsp->{evalue}; $self->element({'Name' => 'Hsp_evalue2', 'Data' => $hsp->{evalue2} } ) if exists $hsp->{evalue2}; $self->element({'Name' => 'Hsp_bit-score', 'Data' => $hsp->{bits} } ) if exists $hsp->{bits}; $self->element({'Name' => 'Hsp_sw-score', 'Data' => $hsp->{'n-w'} } ) if exists $hsp->{'n-w'}; $self->element({'Name' => 'Hsp_sw-score', 'Data' => $hsp->{sw} } ) if exists $hsp->{sw}; $self->element({'Name' => 'Hsp_gaps', 'Data' => $hsp->{'%_gid'} } ) if exists $hsp->{'%_gid'}; $self->element({ 'Name' => 'Hsp_identity', 'Data' => sprintf( "%.0f", $hsp->{'%_id'} * $hsp->{alen} ) }) if ( exists $hsp->{'%_id'} && exists $hsp->{alen} ); if ( exists $hsp->{'%_gid'} ) { $self->element( { 'Name' => 'Hsp_positive', 'Data' => sprintf( "%.0f", $hsp->{'%_gid'} * $hsp->{alen} ) } ) if exists $hsp->{'%_gid'} && exists $hsp->{alen}; } else { $self->element( { 'Name' => 'Hsp_positive', 'Data' => sprintf( "%.0f", $hsp->{'%_id'} * $hsp->{alen} ) } ) if ( exists $hsp->{'%_id'} && exists $hsp->{alen} ); } $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $hsp->{alen} } ) if exists $hsp->{alen}; $self->element( { 'Name' => 'Hsp_query-from', 'Data' => $hsp->{an0} } ) if exists $hsp->{an0}; $self->element( { 'Name' => 'Hsp_query-to', 'Data' => $hsp->{ax0} } ) if exists $hsp->{ax0}; $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => $hsp->{an1} } ) if exists $hsp->{an1}; $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => $hsp->{ax1} } ) if exists $hsp->{ax1}; $self->element( { 'Name' => 'Hsp_querygaps', 'Data' => $hsp->{qgaps} } ) if exists $hsp->{qgaps}; $self->element( { 'Name' => 'Hsp_hitgaps', 'Data' => $hsp->{lgaps} } ) if exists $hsp->{lgaps}; if ( $self->{'_reporttype'} =~ m/^FAST[NXY]$/o ) {
if ( 8 == scalar grep { exists $hsp->{$_} }
qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) ) {
if ( $hsp->{ax0} < $hsp->{an0} ) {
$self->element(
{
'Name' => 'Hsp_query-frame',
'Data' =>
"-@{[(($hsp->{px0} - $hsp->{ax0}) % 3) + 1]}"
}
);
} else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => "+@{[(($hsp->{an0} - $hsp->{pn0}) % 3) + 1]}" } ); } if ( $hsp->{ax1} < $hsp->{an1} ) { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "-@{[(($hsp->{px1} - $hsp->{ax1}) % 3) + 1]}" } ); } else { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "+@{[(($hsp->{an1} - $hsp->{pn1}) % 3) + 1]}" } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => $hsp->{lframe} } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => 0 } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => 0 } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => $hsp->{lframe} } ); } $self->end_element( { 'Name' => 'Hsp' } ); } $self->end_element( { 'Name' => 'Hit' } ); } } 1;
}
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 Stajich, Aaron Mackey, William PearsonTop
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::fasta->new();
Function: Builds a new Bio::SearchIO::fasta object
Returns : Bio::SearchIO::fasta
Args : -idlength - set ID length to something other
than the default (6), this is only
necessary if you have compiled FASTA
with a new default id length to display
in the HSP alignment blocks