Bio::SearchIO::Writer::TextResultWriter - Object to implement writing
Index
Code Index:
NAME
Bio::SearchIO::Writer::TextResultWriter - Object to implement writing
a Bio::Search::ResultI in Text.
SYNOPSIS
use Bio::SearchIO;
use Bio::SearchIO::Writer::TextResultWriter;
my $in = Bio::SearchIO->new(-format => 'blast',
-file => shift @ARGV);
my $writer = Bio::SearchIO::Writer::TextResultWriter->new();
my $out = Bio::SearchIO->new(-writer => $writer);
$out->write_result($in->next_result);
DESCRIPTION
This object implements the SearchWriterI interface which will produce
a set of Text for a specific Bio::Search::Report::ReportI interface.
You can also provide the argument -filters => \%hash to filter the at
the hsp, hit, or result level. %hash is an associative array which
contains any or all of the keys (HSP, HIT, RESULT). The values
pointed to by these keys would be references to a subroutine which
expects to be passed an object - one of Bio::Search::HSP::HSPI,
Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI respectively.
Each function needs to return a boolean value as to whether or not the
passed element should be included in the output report - true if it is
to be included, false if it to be omitted.
For example to filter on sequences in the database which are too short
for your criteria you would do the following.
Define a hit filter method
sub hit_filter {
my $hit = shift;
return $hit->length E<gt> 100; # test if length of the hit sequence
# long enough
}
my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
-filters => { 'HIT' =E<gt> \&hit_filter }
);
Another example would be to filter HSPs on percent identity, let's
only include HSPs which are 75% identical or better.
sub hsp_filter {
my $hsp = shift;
return $hsp->percent_identity E<gt> 75;
}
my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
-filters => { 'HSP' =E<gt> \&hsp_filter }
);
See Bio::SearchIO::SearchWriterI for more info on the filter method.
This module will use the module Text::Wrap if it is installed to wrap
the Query description line. If you do not have Text::Wrap installed
this module will work fine but you won't have the Query line wrapped.
You will see a warning about this when you first instantiate a
TextResultWriter - to avoid these warnings from showing up, simply set
the verbosity upon initialization to -1 like this: my $writer = new
Bio::SearchIO::Writer::TextResultWriter(-verbose => -1);
FEEDBACK
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
Support
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 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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::SearchIO::Writer::TextResultWriter->new();
Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object
Returns : Bio::SearchIO::Writer::TextResultWriter
Args : -filters => hashref with any or all of the keys (HSP HIT RESULT)
which have values pointing to a subroutine reference
which will expect to get a Hit,HSP, Result object respectively
-no_wublastlinks => boolean. Do not display WU-BLAST lines even if
they are parsed out
Links = (1)
to_string
Purpose : Produces data for each Search::Result::ResultI in a string.
: This is an abstract method. For some useful implementations,
: see ResultTableWriter.pm, HitTableWriter.pm,
: and HSPTableWriter.pm.
Usage : print $writer->to_string( $result_obj, @args );
Argument : $result_obj = A Bio::Search::Result::ResultI object
: @args = any additional arguments used by your implementation.
Returns : String containing data for each search Result or any of its
: sub-objects (Hits and HSPs).
Throws : n/a
start_report
Title : start_report
Usage : $index->start_report( CODE )
Function: Stores or returns the code to
write the start of the <HTML> block, the <TITLE> block
and the start of the <BODY> block of HTML. Useful
for (for instance) specifying alternative
HTML if you are embedding the output in
an HTML page which you have already started.
(For example a routine returning a null string).
Returns \&default_start_report (see below) if not
set.
Example : $index->start_report( \&my_start_report )
Returns : ref to CODE if called without arguments
Args : CODE
default_start_report
Title : default_start_report
Usage : $self->default_start_report($result)
Function: The default method to call when starting a report.
Returns : sting
Args : First argument is a Bio::Search::Result::ResultI
title
Title : title
Usage : $self->title($CODE)
Function: Stores or returns the code to provide HTML for the given
BLAST report that will appear at the top of the BLAST report
HTML output. Useful for (for instance) specifying
alternative routines to write your own titles.
Returns \&default_title (see below) if not
set.
Example : $index->title( \&my_title )
Returns : ref to CODE if called without arguments
Args : CODE
default_title
Title : default_title
Usage : $self->default_title($result)
Function: Provides HTML for the given BLAST report that will appear
at the top of the BLAST report output.
Returns : empty for text implementation
Args : First argument is a Bio::Search::Result::ResultI
introduction
Title : introduction
Usage : $self->introduction($CODE)
Function: Stores or returns the code to provide HTML for the given
BLAST report detailing the query and the
database information.
Useful for (for instance) specifying
routines returning alternative introductions.
Returns \&default_introduction (see below) if not
set.
Example : $index->introduction( \&my_introduction )
Returns : ref to CODE if called without arguments
Args : CODE
default_introduction
Title : default_introduction
Usage : $self->default_introduction($result)
Function: Outputs HTML to provide the query
and the database information
Returns : string containing HTML
Args : First argument is a Bio::Search::Result::ResultI
Second argument is string holding literature citation
end_report
Title : end_report
Usage : $self->end_report()
Function: The method to call when ending a report, this is
mostly for cleanup for formats which require you to
have something at the end of the document (</BODY></HTML>)
for HTML
Returns : string
Args : none
id_parser
Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
parser for different flavours of FASTA file.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
description line. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE
default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser( $header )
Function: The default Fasta ID parser for Fasta.pm
Returns $1 from applying the regexp /^>\s*(\S+)/
to $header.
Returns : ID string
Args : a fasta header line string
algorithm_reference
Title : algorithm_reference
Usage : my $reference = $writer->algorithm_reference($result);
Function: Returns the appropriate Bibliographic reference for the
algorithm format being produced
Returns : String
Args : L<Bio::Search::Result::ResultI> to reference
Methods Bio::SearchIO::SearchWriterI
filter
Title : filter
Usage : $writer->filter('hsp', \&hsp_filter);
Function: Filter out either at HSP,Hit,or Result level
Returns : none
Args : string => data type,
CODE reference
no_wublastlinks
Title : no_wublastlinks
Usage : $obj->no_wublastlinks($newval)
Function: Get/Set boolean value regarding whether or not to display
Link = (1)
type output in the report output (WU-BLAST only)
Returns : boolean
Args : on set, new boolean value (a scalar or undef, optional)
#
# BioPerl module for Bio::SearchIO::Writer::TextResultWriter
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
# Let the code begin...
package Bio::SearchIO::Writer::TextResultWriter;
use vars qw($MaxNameLen $MaxDescLen $AlignmentLineWidth $DescLineLen $TextWrapLoaded);
use strict;
# Object preamble - inherits from Bio::Root::RootI
BEGIN {
$MaxDescLen = 65;
$AlignmentLineWidth = 60;
eval { require Text::Wrap; $TextWrapLoaded = 1;};
if( $@ ) {
$TextWrapLoaded = 0;
}
}
use POSIX;
use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI);
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($filters,$nowublastlinks) = $self->_rearrange([qw(FILTERS
NO_WUBLASTLINKS)],
@args);
if( defined $filters ) {
if( !ref($filters) =~ /HASH/i ) {
$self->warn("Did not provide a hashref for the FILTERS option, ignoring.");
} else {
while( my ($type,$code) = each %{$filters} ) {
$self->filter($type,$code);
}
}
}
$self->no_wublastlinks(! $nowublastlinks);
unless( $TextWrapLoaded ) {
$self->warn("Could not load Text::Wrap - the Query Description will not be line wrapped\n");
} else {
$Text::Wrap::columns = $MaxDescLen;
}
return $self;
}
sub to_string {
my ($self,$result,$num) = @_;
$num ||= 0;
return unless defined $result;
my $links = $self->no_wublastlinks;
my ($resultfilter,$hitfilter, $hspfilter) = ( $self->filter('RESULT'),
$self->filter('HIT'),
$self->filter('HSP') );
return '' if( defined $resultfilter && ! &{$resultfilter}($result) );
my ($qtype,$dbtype,$dbseqtype,$type);
my $alg = $result->algorithm;
my $wublast = ($result->algorithm_version =~ /WashU/) ? 1 : 0;
# This is actually wrong for the FASTAs I think
if( $alg =~ /T(FAST|BLAST)([XY])/i ) {
$qtype = $dbtype = 'translated';
$dbseqtype = $type = 'PROTEIN';
} elsif( $alg =~ /T(FAST|BLAST)N/i ) {
$qtype = '';
$dbtype = 'translated';
$type = 'PROTEIN';
$dbseqtype = 'NUCLEOTIDE';
} elsif( $alg =~ /(FAST|BLAST)N/i ||
$alg =~ /(WABA|EXONERATE)/i ) {
$qtype = $dbtype = '';
$type = $dbseqtype = 'NUCLEOTIDE';
} elsif( $alg =~ /(FAST|BLAST)P/ ||
$alg =~ /SSEARCH|(HMM|SEARCH|PFAM)/i ) {
$qtype = $dbtype = '';
$type = $dbseqtype = 'PROTEIN';
} elsif( $alg =~ /(FAST|BLAST)[XY]/i ) {
$qtype = 'translated';
$dbtype = 'PROTEIN';
$dbseqtype = $type = 'PROTEIN';
} else {
print STDERR "algorithm was ", $result->algorithm, " couldn't match\n";
}
my %baselens = ( 'Sbjct:' => ( $dbtype eq 'translated' ) ? 3 : 1,
'Query:' => ( $qtype eq 'translated' ) ? 3 : 1);
my $str;
if( ! defined $num || $num <= 1 ) {
$str = &{$self->start_report}($result);
}
$str .= &{$self->title}($result);
$str .= $result->algorithm . " " . $result->algorithm_version . "\n\n\n";
$str .= $result->algorithm_reference || $self->algorithm_reference($result);
$str .= &{$self->introduction}($result);
$str .= qq{
Score E
Sequences producing significant alignments: (bits) value
};
my $hspstr = '';
if( $result->can('rewind')) {
$result->rewind(); # support stream based parsing routines
}
while( my $hit = $result->next_hit ) {
next if( defined $hitfilter && ! &{$hitfilter}($hit) );
my $nm = $hit->name();
$self->debug( "no $nm for name (".$hit->description(). "\n")
unless $nm;
my ($gi,$acc) = &{$self->id_parser}($nm);
my $p = "%-$MaxDescLen". "s";
my $descsub;
my $desc = sprintf("%s %s",$nm,$hit->description);
if( length($desc) - 3 > $MaxDescLen) {
$descsub = sprintf($p,
substr($desc,0,$MaxDescLen-3) .
"...");
} else {
$descsub = sprintf($p,$desc);
}
$str .= $wublast ? sprintf("%s %-4s %s\n",
$descsub,
defined $hit->raw_score ? $hit->raw_score : ' ',
defined $hit->significance ? $hit->significance : '?') :
sprintf("%s %-4s %s\n",
$descsub,
defined $hit->bits ? $hit->bits: ' ',
defined $hit->significance ? $hit->significance : '?');
my @hsps = $hit->hsps;
if( @hsps ) {
$hspstr .= sprintf(">%s %s\n%9sLength = %d\n\n",
$hit->name,
defined $hit->description ? $hit->description : '',
'', # empty is for the %9s in the str formatting
$hit->length);
foreach my $hsp ( @hsps ) {
next if( defined $hspfilter && ! &{$hspfilter}($hsp) );
$hspstr .= sprintf(" Score = %4s bits (%s), Expect = %s",
$hsp->bits, $hsp->score, $hsp->evalue);
if( $hsp->pvalue ) {
$hspstr .= ", P = ".$hsp->pvalue;
}
$hspstr .= "\n";
$hspstr .= sprintf(" Identities = %d/%d (%d%%)",
( $hsp->frac_identical('total') *
$hsp->length('total')),
$hsp->length('total'),
POSIX::floor($hsp->frac_identical('total')
* 100));
if( $type eq 'PROTEIN' ) {
$hspstr .= sprintf(", Positives = %d/%d (%d%%)",
( $hsp->frac_conserved('total') *
$hsp->length('total')),
$hsp->length('total'),
POSIX::floor($hsp->frac_conserved('total') * 100));
}
if( $hsp->gaps ) {
$hspstr .= sprintf(", Gaps = %d/%d (%d%%)",
$hsp->gaps('total'),
$hsp->length('total'),
POSIX::floor(100 * $hsp->gaps('total') /
$hsp->length('total')));
}
$hspstr .= "\n";
my ($hframe,$qframe) = ( $hsp->hit->frame,
$hsp->query->frame);
my ($hstrand,$qstrand) = ($hsp->hit->strand,$hsp->query->strand);
# so TBLASTX will have Query/Hit frames
# BLASTX will have Query frame
# TBLASTN will have Hit frame
if( $hstrand || $qstrand ) {
$hspstr .= " Frame = ";
my ($signq, $signh);
unless( $hstrand ) {
$hframe = undef;
# if strand is null or 0 then it is protein
# and this no frame
} else {
$signh = $hstrand < 0 ? '-' : '+';
}
unless( $qstrand ) {
$qframe = undef;
# if strand is null or 0 then it is protein
} else {
$signq =$qstrand < 0 ? '-' : '+';
}
# remember bioperl stores frames as 0,1,2 (GFF way)
# BLAST reports reports as 1,2,3 so
# we have to add 1 to the frame values
if( defined $hframe && ! defined $qframe) {
$hspstr .= "$signh".($hframe+1);
} elsif( defined $qframe && ! defined $hframe) {
$hspstr .= "$signq".($qframe+1);
} else {
$hspstr .= sprintf(" %s%d / %s%d",
$signq,$qframe+1,
$signh, $hframe+1);
}
}
if( $links &&
$hsp->can('links') && defined(my $lnks = $hsp->links) ) {
$hspstr .= sprintf(" Links = %s\n",$lnks);
}
$hspstr .= "\n\n";
my @hspvals = ( {'name' => 'Query:',
'seq' => $hsp->query_string,
'start' => ( $qstrand >= 0 ?
$hsp->query->start :
$hsp->query->end),
'end' => ($qstrand >= 0 ?
$hsp->query->end :
$hsp->query->start),
'index' => 0,
'direction' => $qstrand || 1
},
{ 'name' => ' 'x6, # this might need to adjust for long coordinates??
'seq' => $hsp->homology_string,
'start' => undef,
'end' => undef,
'index' => 0,
'direction' => 1
},
{ 'name' => 'Sbjct:',
'seq' => $hsp->hit_string,
'start' => ($hstrand >= 0 ?
$hsp->hit->start : $hsp->hit->end),
'end' => ($hstrand >= 0 ?
$hsp->hit->end : $hsp->hit->start),
'index' => 0,
'direction' => $hstrand || 1
}
);
# let's set the expected length (in chars) of the starting number
# in an alignment block so we can have things line up
# Just going to try and set to the largest
my ($numwidth) = sort { $b <=> $a }(length($hspvals[0]->{'start'}),
length($hspvals[0]->{'end'}),
length($hspvals[2]->{'start'}),
length($hspvals[2]->{'end'}));
my $count = 0;
while ( $count <= $hsp->length('total') ) {
foreach my $v ( @hspvals ) {
my $piece = substr($v->{'seq'}, $v->{'index'} +$count,
$AlignmentLineWidth);
my $cp = $piece;
my $plen = scalar ( $cp =~ tr/\-//);
my ($start,$end) = ('','');
if( defined $v->{'start'} ) {
$start = $v->{'start'};
# since strand can be + or - use the direction
# to signify which whether to add or substract from end
my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )*
$baselens{$v->{'name'}};
if( length($piece) < $AlignmentLineWidth ) {
$d = (length($piece) - $plen) * $v->{'direction'} *
$baselens{$v->{'name'}};
}
$end = $v->{'start'} + $d - $v->{'direction'};
$v->{'start'} += $d;
}
$hspstr .= sprintf("%s %-".$numwidth."s %s %s\n",
$v->{'name'},
$start,
$piece,
$end
);
}
$count += $AlignmentLineWidth;
$hspstr .= "\n";
}
}
$hspstr .= "\n";
}
}
$str .= "\n\n".$hspstr;
$str .= sprintf(qq{ Database: %s
Posted date: %s
Number of letters in database: %s
Number of sequences in database: %s
Matrix: %s
},
$result->database_name(),
$result->get_statistic('posted_date') ||
POSIX::strftime("%b %d, %Y %I:%M %p",localtime),
&_numwithcommas($result->database_letters()),
&_numwithcommas($result->database_entries()),
$result->get_parameter('matrix') || '');
if( defined (my $open = $result->get_parameter('gapopen')) ) {
$str .= sprintf("Gap Penalties Existence: %d, Extension: %d\n",
$open || 0, $result->get_parameter('gapext') || 0);
}
# skip those params we've already output
foreach my $param ( grep { ! /matrix|gapopen|gapext/i }
$result->available_parameters ) {
$str .= "$param: ". $result->get_parameter($param) ."\n";
}
$str .= "Search Statistics\n";
# skip posted date, we already output it
foreach my $stat ( sort grep { ! /posted_date/ }
$result->available_statistics ) {
my $expect = $result->get_parameter('expect');
my $v = $result->get_statistic($stat);
if( $v =~ /^\d+$/ ) {
$v = &_numwithcommas($v);
}
if( defined $expect &&
$stat eq 'seqs_better_than_cutoff' ) {
$str .= "seqs_better_than_$expect: $v\n";
} else {
my $v =
$str .= "$stat: $v\n";
}
}
$str .= "\n\n";
return $str;
}
sub start_report {
my( $self, $code ) = @_;
if ($code) {
$self->{'_start_report'} = $code;
}
return $self->{'_start_report'} || \&default_start_report;
}
sub default_start_report {
my ($result) = @_;
return "";
}
sub title {
my( $self, $code ) = @_;
if ($code) {
$self->{'_title'} = $code;
}
return $self->{'_title'} || \&default_title;
}
sub default_title {
my ($result) = @_;
return "";
# The HTML implementation
# return sprintf(
# qq{<CENTER><H1><a href="http://bioperl.org">Bioperl</a> Reformatted HTML of %s Search Report<br> for %s</H1></CENTER>},
# $result->algorithm,
# $result->query_name());
}
sub introduction {
my( $self, $code ) = @_;
if ($code) {
$self->{'_introduction'} = $code;
}
return $self->{'_introduction'} || \&default_introduction;
}
sub default_introduction {
my ($result) = @_;
return sprintf(
qq{
Query= %s
(%s letters)
Database: %s
%s sequences; %s total letters
},
&_linewrap($result->query_name . " " .
$result->query_description),
&_numwithcommas($result->query_length),
$result->database_name(),
&_numwithcommas($result->database_entries()),
&_numwithcommas($result->database_letters()),
);
}
sub end_report {
return "";
}
# copied from Bio::Index::Fasta
# useful here as well
sub id_parser {
my( $self, $code ) = @_;
if ($code) {
$self->{'_id_parser'} = $code;
}
return $self->{'_id_parser'} || \&default_id_parser;
}
sub default_id_parser {
my ($string) = @_;
my ($gi,$acc);
if( $string =~ s/gi\|(\d+)\|?// )
{ $gi = $1; $acc = $1;}
if( $string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/ ) {
$acc = defined $2 ? $2 : $1;
} else {
$acc = $string;
$acc =~ s/^\s+(\S+)/$1/;
$acc =~ s/(\S+)\s+$/$1/;
}
return ($gi,$acc);
}
sub MIN { $a <=> $b ? $a : $b; }
sub MAX { $a <=> $b ? $b : $a; }
sub algorithm_reference{
my ($self,$result) = @_;
return '' if( ! defined $result || !ref($result) ||
! $result->isa('Bio::Search::Result::ResultI')) ;
if( $result->algorithm =~ /BLAST/i ) {
my $res = $result->algorithm . ' '. $result->algorithm_version. "\n";
if( $result->algorithm_version =~ /WashU/i ) {
return $res .qq{
Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.
Reference: Gish, W. (1996-2000) http://blast.wustl.edu
};
} else {
return $res . qq{
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
};
}
} elsif( $result->algorithm =~ /FAST/i ) {
return $result->algorithm. " ". $result->algorithm_version . "\n".
"\nReference: Pearson et al, Genomics (1997) 46:24-36\n";
} else {
return '';
}
}
# from Perl Cookbook 2.17
sub _numwithcommas {
my $num = reverse( $_[0] );
$num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g;
return scalar reverse $num;
}
sub _linewrap {
my ($str) = @_;
if($TextWrapLoaded) {
return Text::Wrap::wrap("","",$str); # use Text::Wrap
} else { return $str; } # cannot wrap
}
sub no_wublastlinks{
my $self = shift;
return $self->{'no_wublastlinks'} = shift if @_;
return $self->{'no_wublastlinks'};
}
1;