/usr/lib/perl5/Zerg/Report.pm is in libzerg-perl 1.0.4-2build1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 | # Copyright (C) 2002 Apuã Paquola, Abimael Machado - Instituto de Química -
# Universidade de São Paulo - Brasil
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
package Zerg::Report;
use strict;
use Carp;
use Zerg;
our $VERSION = '1.0.4';
sub new
{
my $self = { };
my $class = shift;
my $file = shift;
if( defined($file) ){ Zerg::zerg_open_file($file); }
Zerg::zerg_unignore_all();
bless $self,$class;
return $self;
}
sub getReport
{
my $self=shift;
my $blast_report = undef;
my ($c,$v,$hit_counter,$hsp_counter);
$hit_counter=-1;
$hsp_counter=-1;
while((($c, $v)= Zerg::zerg_get_token()) && $c)
{
if( !defined($blast_report) ){ $blast_report = {}; }
if($c==BLAST_VERSION)
{
$blast_report->{blast_version}=$v;
$blast_report->{byte_offset}=Zerg::zerg_get_token_offset();
$hit_counter=-1;
}
elsif($c==QUERY_NAME)
{
$blast_report->{query_name}=$v;
}
elsif($c==QUERY_ANNOTATION)
{
$blast_report->{query_annotation}=$v;
}
elsif($c==QUERY_LENGTH)
{
$blast_report->{query_length}=$v;
}
elsif($c==SUBJECT_NAME)
{
$hit_counter++;
$hsp_counter=-1;
$blast_report->{hits}[$hit_counter]{"subject_name"}=$v;
}
elsif($c==SUBJECT_ANNOTATION)
{
$blast_report->{hits}[$hit_counter]{"subject_annotation"}=$v;
}
elsif($c==SUBJECT_LENGTH)
{
$blast_report->{hits}[$hit_counter]{"subject_length"}=$v;
}
elsif($c==SCORE_BITS)
{
$hsp_counter++;
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score_bits"}=$v;
}
elsif($c==SCORE)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score"}=$v;
}
elsif($c==EVALUE)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"evalue"}=$v;
}
elsif($c==IDENTITIES)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"identities"}=$v;
}
elsif($c==ALIGNMENT_LENGTH)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"alignment_length"}=$v;
}
elsif($c==PERCENT_IDENTITIES)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_identities"}=$v;
}
elsif($c==GAPS)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"gaps"}=$v;
}
elsif($c==QUERY_ORIENTATION)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_orientation"}=$v;
}
elsif($c==SUBJECT_ORIENTATION)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_orientation"}=$v;
}
elsif($c==QUERY_START)
{
if( $v && !$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"}=$v; }
}
elsif($c==QUERY_ALI)
{
if( $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_ali"} .= $v; }
}
elsif($c==QUERY_END)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_end"}=$v;
}
elsif($c==SUBJECT_START)
{
if( $v && !$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"}=$v; }
}
elsif($c==SUBJECT_ALI)
{
if( $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_ali"} .= $v; }
}
elsif($c==SUBJECT_END)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_end"}=$v;
}
elsif($c==POSITIVES)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"positives"}=$v;
}
elsif($c==PERCENT_POSITIVES)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_positives"}=$v;
}
elsif($c==QUERY_FRAME)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_frame"}=$v;
}
elsif($c==SUBJECT_FRAME)
{
$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_frame"}=$v;
}
elsif($c==ROUND_NUMBER)
{
$blast_report->{round_begins}[$v-1] = $hit_counter + 1;
}
elsif($c==UNMATCHED)
{
confess("Syntax error in blast report: '$v'");
}
elsif($c==END_OF_REPORT)
{
return $blast_report;
}
}
return $blast_report;
}
sub closeFile
{
Zerg::zerg_close_file();
}
1;
# 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 Zerg::Report ':all';
# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
# will save memory.
# Preloaded methods go here.
# Autoload methods go after =cut, and are processed by the autosplit program.
__END__
# Below is stub documentation for your module. You better edit it!
=head1 NAME
Zerg::Report - get attributes from a BLAST file in a data structure
=head1 SYNOPSIS
use Zerg::Report;
my $zerg_report = new Zerg::Report("output.blastn");
while($r=$zerg_report->getReport())
{
foreach my $hit (@{$r->{hits}})
{
foreach my $hsp (@{$hit->{hsps}})
{
print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}\n";
}
}
}
$zerg_report->closeFile();
=head1 DESCRIPTION
Zerg::Report uses Zerg to parse a file - or STDIN if file is not given -
containing one or multiple BLAST reports and, for each report, stores
the obtained fields in a data structure made of arrays and hashes.
Please consult the Zerg man page to see which fields are extracted.
The method getReport() reads a BLAST report from the input file and
returns a reference to a data structure like the one in the example
below. When no report is found, it returns undef. It dies from
syntax errors in BLAST reports with a stack backtrace.
Example of a data structure returned by getReport():
$r = {
'query_name' => 'ME1-0081T-R227-B12-U.G',
'blast_version' => 'BLASTX 1.3.6 [2002-03-05]',
'byte_offset' => 4981,
'query_length' => '444',
'query_annotation' => ''
'round_begins' => [ 0, 129, 201 ], # indicates the first hit in each round of iterated blast
'hits' => [
{
'subject_annotation' => '(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD-e]',
'hsps' => [
{
'query_end' => '82',
'subject_ali' => 'ASELEIFAALIECEA-GSTDYDGMLAVASVVMNRVNHRYYPDTITGVIYQSGQFSPVASGKLDKVLKRGIKSSCLEVAKDA',
'query_ali' => 'DAQTRKLAAIAYGEASGANDANEIGGIAWAVANRARAWGGK-TVDGLLAADPNYTYAVKDG-NQRYAKLMKATEAAIAADP',
'subject_end' => '328',
'identities' => '15',
'score' => '87',
'percent_positives' => '41',
'gaps' => '3',
'score_bits' => '37.9',
'alignment_length' => '81',
'evalue' => '0.40',
'percent_identities' => '18',
'positives' => '34',
'query_start' => '4',
'subject_start' => '249'
}
],
'subject_length' => '880',
'subject_name' => 'gi|16802882|ref|NP_464367.1|'
},
],
};
=head1 AUTHORS
Apuã Paquola <apua@iq.usp.br>, Abimael Machado <abimael@iq.usp.br> IQ-USP Bioinformatics Lab
Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich
=head1 SEE ALSO
Zerg
=cut
# vim:et:ts=2:ai:
|