This file is indexed.

/usr/bin/bp_seqfeature_load is in bioperl 1.6.923-1.

This file is owned by root:root, with mode 0o755.

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
#!/usr/bin/perl 

eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
    if 0; # not running under some shell

use strict;
use warnings;

## Used to output the 'usage' message
use Pod::Usage;

## Used to parse command line options
use Getopt::Long;

## Used to create temporary files, if necessary
use File::Spec;

## BioPerl!
use Bio::DB::SeqFeature::Store;
use Bio::DB::SeqFeature::Store::GFF3Loader;



## The available options. Note, these defaults are 'hard coded' into
## the USAGE POD, so if you change one of the defaults (you shouldn't),
## you should update the USAGE.

my $DSN			= 'dbi:mysql:test';
my $SFCLASS		= 'Bio::DB::SeqFeature';
my $ADAPTOR		= 'DBI::mysql';
my $NAMESPACE;
my $VERBOSE		= 1;
my $FAST		= 0;
my $TMP			= File::Spec->tmpdir();
my $IGNORE_SEQREGION	= 0;
my $CREATE		= 0;
my $USER 		= '';
my $PASS 		= '';
my $COMPRESS		= 0;
my $INDEX_SUB		= 1;
my $NOALIAS_TARGET	= 0;
my $SUMMARY_STATS	= 0;
my $NOSUMMARY_STATS  = 0;

## Two flags based on http://stackoverflow.com/questions/1232116
## how-to-create-pod-and-use-pod2usage-in-perl
my $opt_help;
my $opt_man;

GetOptions( 'd|dsn=s'			=> \$DSN,
	    's|seqfeature=s'		=> \$SFCLASS,
	    'n|namespace=s'		=> \$NAMESPACE,
	    'a|adaptor=s'		=> \$ADAPTOR,
	    'v|verbose!'		=> \$VERBOSE,
	    'f|fast'			=> \$FAST,
	    'T|temporary-directory=s'	=> \$TMP,
	    'i|ignore-seqregion'	=> \$IGNORE_SEQREGION,
	    'c|create'			=> \$CREATE,
	    'u|user=s'			=> \$USER,
	    'p|password=s'		=> \$PASS,
	    'z|zip'			=> \$COMPRESS,
	    'S|subfeatures!'		=> \$INDEX_SUB,

	    ## Any good single letter choices here?
	    'noalias-target'		=> \$NOALIAS_TARGET,
	    'summary'			=> \$SUMMARY_STATS,
        'N|nosummary'    => \$NOSUMMARY_STATS,

	    ## I miss '--help' when it isn't there!
	    'h|help!'			=> \$opt_help,
	    'm|man!'			=> \$opt_man,
	  )
  or pod2usage( -message =>
		"\nTry 'bp_seqfeature_load.pl --help' for more information\n",
		-verbose => 0,
		-exitval => 2,
	      );

## Should we output usage information?
pod2usage( -verbose => 1 ) if $opt_help;
pod2usage( -verbose => 2 ) if $opt_man;

## Did we get any files to process?
@ARGV
  or pod2usage( -message =>
		"\nYou need to pass some GFF or fasta files to load\n",
		-verbose => 0,
		-exitval => 2,
	      );



## POD

=head1 NAME

bp_seqfeature_load.pl - Load GFF into a SeqFeature database

=head1 DESCRIPTION

Pass any number of GFF or fasta format files (or GFF with embedded
fasta) to load the features and sequences into a SeqFeature
database. The database (and adaptor) to use is specified on the
command line. Use the --create flag to create a new SeqFeature
database.

=head1 SYNOPSIS

 bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]

Try 'bp_seqfeature_load.pl --help' or '--man' for more information.

=head1 OPTIONS

=over 4

=item -d, --dsn

DBI data source (default dbi:mysql:test)

=item -n, --namespace

The table prefix to use (default undef) Allows several independent
sequence feature databases to be stored in a single database

=item -s, --seqfeature

The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)

=item -a, --adaptor

The storage adaptor (class) to use (default DBI::mysql)

=item -v, --verbose

Turn on verbose progress reporting (default true) Use --noverbose to
switch this off.

=item -f, --fast

Activate fast loading. (default 0) Only available for some adaptors.

=item -T, --temporary-directory

Specify temporary directory for fast loading (default
File::Spec->tmpdir())

=item -i, --ignore-seqregion

If true, then ignore ##sequence-region directives in the GFF3 file
(default, create a feature for each region)

=item -c, --create

Create the database and reinitialize it (default false) Note, this
will erase previous database contents, if any.

=item -u, --user

User to connect to database as

=item -p, --password

Password to use to connect to database

=item -z, --zip

Compress database tables to save space (default false)

=item -S, --subfeatures

Turn on indexing of subfeatures (default true) Use --nosubfeatures to
switch this off.

=item --summary

Generate summary statistics for coverage graphs (default false) This
can be run on a previously loaded database or during the load. It will
default to true if --create is used.

=item -N, --nosummary

Do not generate summary statistics to save some space and load time (default if
--create is not specified, use this option to explicitly turn off summary
statistics when --create is specified)

=item --noalias-target

Don't create an Alias attribute whose value is the target_id in a
Target attribute (if the feature contains a Target attribute, the
default is to create an Alias attribute whose value is the target_id
in the Target attribute)

=back

Please see http://www.sequenceontology.org/gff3.shtml for information
about the GFF3 format. BioPerl extends the format slightly by adding a
##index-subfeatures directive. Set this to a true value if you wish
the database to be able to retrieve a feature's individual parts (such
as the exons of a transcript) independently of the top level feature:

  ##index-subfeatures 1

It is also possible to control the indexing of subfeatures on a
case-by-case basis by adding "index=1" or "index=0" to the feature's
attribute list. This should only be used for subfeatures.

Subfeature indexing is true by default. Set to false (0) to save lots
of database space and speed performance. You may use --nosubfeatures
to force this.

=cut





if ($FAST) {
  -d $TMP && -w $TMP
    or die "Fast loading is requested, but I cannot write into the directory $TMP";
  $DSN .= ";mysql_local_infile=1" if $ADAPTOR =~ /mysql/i && $DSN !~ /mysql_local_infile/;
}

my @options;
@options = ($USER,$PASS) if $USER || $PASS;

my $store = Bio::DB::SeqFeature::Store->new
(
    -dsn        => $DSN,
    -namespace  => $NAMESPACE,
    -adaptor    => $ADAPTOR,
    -tmpdir     => $TMP,
    -user       => $USER,
    -pass       => $PASS,
    -write      => 1,
    -create     => $CREATE,
    -compress   => $COMPRESS,
)
or die "Couldn't create connection to the database";

$store->init_database('erase') if $CREATE;
$SUMMARY_STATS++               if $CREATE; # this is a good thing

my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new
(
    -store              => $store,
    -sf_class           => $SFCLASS,
    -verbose            => $VERBOSE,
    -tmpdir             => $TMP,
    -fast               => $FAST,
    -ignore_seqregion   => $IGNORE_SEQREGION,
    -index_subfeatures  => $INDEX_SUB,
    -noalias_target     => $NOALIAS_TARGET,
    -summary_stats      => $NOSUMMARY_STATS ? 0 : $SUMMARY_STATS,
)
or die "Couldn't create GFF3 loader";

# on signals, give objects a chance to call their DESTROY methods
$SIG{TERM} = $SIG{INT} = sub {  undef $loader; undef $store; die "Aborted..."; };

$loader->load(@ARGV);

exit 0;