/usr/lib/x86_64-linux-gnu/perl5/5.20/RG/Blast/Parser.pm is in librg-blast-parser-perl 0.03-2+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 | # Copyright (C) 2012 by Laszlo Kajan, Technical University of Munich, Germany
#
# This program is free software; you can redistribute it and/or modify
# it under the same terms as Perl itself, either Perl version 5.8.8 or,
# at your option, any later version of Perl 5 you may have available.
package RG::Blast::Parser;
use 5.008008;
use strict;
use warnings;
require Exporter;
use AutoLoader qw(AUTOLOAD);
our @ISA = qw(Exporter);
# Items to export into callers namespace by default. Note: do not export
# names by default without a very good reason. Use EXPORT_OK instead.
# Do not simply export all your public functions/methods/constants.
# This allows declaration use RG::Blast::Parser ':all';
# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
# will save memory.
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
our $VERSION = '0.03';
require XSLoader;
XSLoader::load('RG::Blast::Parser', $VERSION);
# Preloaded methods go here.
# Autoload methods go after =cut, and are processed by the autosplit program.
1;
__END__
# Below is stub documentation for your module. You'd better edit it!
=head1 NAME
RG::Blast::Parser - fast NCBI BLAST parser
=head1 SYNOPSIS
use Data::Dumper;
use RG::Blast::Parser;
my $parser = RG::Blast::Parser->new(); # read from STDIN
open( EXAMPLE, '<', '/usr/share/doc/librg-blast-parser-perl/examples/converged.ali' ) || confess($!);
my $parser = RG::Blast::Parser->new( \*EXAMPLE, "converged.ali" ); # read from EXAMPLE, use name "converged.ali" in error messages
while( my $res = $parser->parse() )
{
print Dumper( $res );
}
eval {
my $res = $parser->parse();
# ...
};
if( $@ && $@ =~ /^parser error/ ) { warn("failed to parse blast result - exception caught"); }
=head1 DESCRIPTION
This package contains perl binding for a very fast C/C++ library for NCBI
BLAST -m 0 (default) output parsing. BLAST results are returned in a
convenient hash structure.
Multiple results may be concatenated for input. One result is parsed and
returned at a time.
=head1 CONSTRUCTOR
=over
=item new( [FILEHANDLE, [NAME]] )
Creates an "RG::Blast::Parser". Blast results are read from FILEHANDLE, STDIN
by default. The input stream may be named NAME in error messages (default:
"STDIN").
=back
=head1 METHODS
=over
=item parse( [TRACE_PARSING, [TRACE_SCANNING]] )
Parse one complete BLAST result and return it. If no results on input stream,
returns "undef". In case of parser error it die()s with an (at present not
very useful) error message.
The following structure is returned in a hash reference:
{
blast_version => STRING,
references => [ STRING, ... ],
rounds => [
{
oneline_idx => NUM, # index of first one-line description of
# this round in "onelines" array
oneline_cnt => NUM, # number of one-line descriptions of
# this round
hit_idx => NUM, # index of first hit of this round in
# "hits" array
hit_cnt => NUM, # number of hits of this round
oneline_new_idx => NUM|undef# index of first new (not-seen-before)
# one-line description of this round
# in "onelines" array
oneline_new_cnt => NUM # number of new one-line descriptions of
# this round
}, ...
],
q_name => STRING,
q_desc => STRING|undef,
q_length => NUM,
db_name => STRING,
db_nseq => NUM,
db_nletter => NUM,
onelines => [ # one-line descriptions from all rounds
{
name => STRING,
desc => STRING|undef,
bit_score => NUM,
e_value => NUM
}, ...
],
converged => BOOLEAN,
hits => [ # hits from all rounds
{
name => STRING,
desc => STRING|undef,
length => NUM,
hsps => [
{
bit_score => NUM,
raw_score => NUM,
e_value => NUM,
method => STRING,
identities => NUM,
positives => NUM,
gaps => NUM,
q_strand => STRING|undef,
s_strand => STRING|undef,
q_frame => NUM|undef,
s_frame => NUM|undef,
q_start => NUM,
q_ali => STRING,
q_end => NUM,
match_line => STRING,
s_start => NUM,
s_ali => STRING,
s_end => NUM
}, ...
]
}, ...
],
tail => STRING # bulk text after the last hit / one-line
# description
}
If you want tracing for parsing and scanning, you can enable them using the
parameters of this call.
=item result()
Returns the last BLAST result parsed or "undef" if no last result.
=item get_trace_scanning()
Returns scan trace state as a Boolean value.
=item set_trace_scanning( BOOLEAN )
Set scan trace - debugging aid.
=back
=head1 SEE ALSO
Zerg(3pm), Zerg::Report(3pm)
=head1 AUTHOR
Laszlo Kajan, E<lt>lkajan@rostlab.orgE<gt>
=head1 COPYRIGHT AND LICENSE
Copyright (C) 2012 by Laszlo Kajan
This program is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.8 or,
at your option, any later version of Perl 5 you may have available.
=cut
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