#
# BioPerl module for Bio::SearchIO::fasta
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO::fasta - A SearchIO parser for FASTA results
=head1 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.
}
=head1 DESCRIPTION
This object contains the event based parsing code for FASTA format
reports. It creates L<Bio::Search::HSP::FastaHSP> objects instead of
L<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:
L<http://bioperl.open-bio.org/wiki/HOWTO:SearchIO>.
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich, Aaron Mackey, William Pearson
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SearchIO::fasta;
use vars qw(%MODEMAP %MAPPING $IDLENGTH);
use strict;
# Object preamble - inherits from Bio::Root::RootI
use Bio::Factory::ObjectFactory;
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' },
);
}
use base qw(Bio::SearchIO);
=head2 new
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
=cut
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;
}
=head2 next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub next_result {
my ($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();
}
=head2 start_element
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'
=cut
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'} = '';
}
}
=head2 end_element
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'
=cut
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;
}
=head2 element
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'
=cut
sub element {
my ( $self, $data ) = @_;
$self->start_element($data);
$self->characters($data);
$self->end_element($data);
}
=head2 characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
=cut
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'};
}
=head2 _mode
Title : _mode
Usage : $obj->_mode($newval)
Function:
Example :
Returns : value of _mode
Args : newvalue (optional)
=cut
sub _mode {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_mode'} = $value;
}
return $self->{'_mode'};
}
=head2 within_element
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
=cut
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;
}
=head2 in_element
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
=cut
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} )
);
}
=head2 start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handles a start document event
Returns : none
Args : none
=cut
sub start_document {
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'} = undef;
$self->{'_mode'} = '';
$self->{'_elements'} = [];
}
=head2 end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub end_document {
my ( $self, @args ) = @_;
return $self->{'_result'};
}
=head2 idlength
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)
=cut
sub idlength {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_idlength'} = $value;
}
return $self->{'_idlength'} || $IDLENGTH;
}
=head2 result_count
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
=cut
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
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;
}
=head2 _will_handle
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:
=over 2
=item 1
Using the cached pointer to the EventHandler to minimize repeated
lookups.
=item 2
Caching the will_handle status for each type that is encountered so
that it only need be checked by calling
handler-E<gt>will_handle($type) once.
=back
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-E<gt>_eventHandler().
=cut
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 ? $handler : undef;
}
=head2 _processHits
Title : _processHits
Usage : Private method. For internal use only.
Function: Process/report any hits/hsps we saw in the top table, not in alignments.
Returns : nothing.
Args : array of hits to process.
=cut
sub _processHits {
my ($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;