NAME

Bio::Grep::SearchResult - Data structure for a back-end search hit

SYNOPSIS

# output the search results with nice alignments
while ( my $res = $sbe->next_res ) {
   # $res->sequence is a Bio::Seq object with down-/upstream regions
   # see Bio::Grep::SearchSettings
   print $res->sequence->id . "\n";
   
   # $res->subject is a Bio::Seq object without down-/upstream regions 
   print $res->subject->seq . "\n";

   # print down-/upstream regions lower case, subject sequence uppercase
   print $res->mark_subject_uppercase() . "\n";
   
   # output alignment
   print $res->alignment_string() . "\n";

   # print coordinates: perldoc Bio::SimpleAlign, Bio::LocatableSeq
   $print $res->alignment->get_seq_by_pos(1)->start . "\n\n";
}

DESCRIPTION

Bio::Grep::SearchResult is the data structure for one hit in the database.

METHODS

new(sequence, begin, end, alignment, sequence_id, remark);

This function constructs a Bio::Grep::SearchResult object. Only called by the back-end parser.

sequence()

Get/set the sequence found in database. Bio::Seq object.

subject()

Get the sequence found in database as string without upstream and downstream regions. Bio::Seq object.

query()

Get the query as Bio::Seq object. Useful for multiple queries.

alignment()

Get/set the alignment of the match. See Bio::SimpleAlign for details. There are powerful modules for converting this module in many formats. See Bio::AlignIO for details.

sequence_id()

Getter/Setter for sequence ID in database. This is an internal ID of the back-end, not any ID of some annotation in the sequence name. The internal ID can be used in the back-end function get_sequences (Bio::Grep::Backend::BackendI).

begin()

Get/set the position of the beginning of the subject in the sequence. This allows retrieving upstream regions from the back-end. First position is 0.

my $seq = $res->sequence->seq;
my $upstream   = substr $seq, 0, $res->begin;
my $subject    = substr $seq, $res->begin, $res->end - $res->begin;
my $downstream = substr $seq, $res->end;

Note that $res->begin differs from $sbe->settings->upstream if the available upstream region is smaller than requested!

end()

Get/set the position of the end of the subject in the sequence. This allows retrieving downstream regions from the back-end. See begin().

dG()

Get/set dG . See Bio::Grep::RNA::HybridizationI for details.

remark()

Get/set some additional informations like filter results to this hit.

evalue()

Get/set the evalue of this hit.

percent_identity()

Get/set the identity in percent of this hit.

OBJECT FORMATTER

Some predefined methods for printing objects.

mark_subject_uppercase()

This function returns the sequence in a string. the substring from $self->begin to $self->end will be in uppercase, the rest in lowercase.

alignment_string()

This function returns a string with the formated alignment. We use CLUSTALW Format without many blank lines and CLUSTAL header. In some back-ends like Agrep, this function will return an empty string if no_alignments is true.

SEE ALSO

Bio::SimpleAlign Bio::LocatableSeq Bio::AlignIO Bio::Seq Bio::SeqIO Bio::Grep::Backend::BackendI

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENCE AND COPYRIGHT

Based on Weigel::Search v0.13

Copyright (C) 2005-2006 by Max Planck Institute for Developmental Biology, Tuebingen.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER OF WARRANTY

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