/usr/bin/bp_index is in bioperl 1.6.924-3.
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 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
=head1 NAME
bp_index.pl - indexes files for use by bp_fetch.pl
=head1 SYNOPSIS
bp_index.pl index_name file1 file2 etc.
=head1 DESCRIPTION
bp_index.pl builds a bioperl index for the sequence files given in the
argument list, under the index name. For example
bp_index.pl nrdb /data/nrdb/nrdb.fasta
would build an index called 'nrdb' as the index name for the file
nrdb.fasta, and
bp_index.pl -fmt EMBL swiss /data/swiss/*.dat
would build an index called swiss for all the files in /data/swiss
which end in .dat which are in EMBL format.
The indexes are built using the Bio/Index/* modules, in particular,
Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which
uses these modules can use the index. A good example script is bp_fetch
which fetches sequences and pipes them to STDOUT, for example
bp_fetch swiss:ROA1_HUMAN
gets the ROA1_HUMAN sequence from the swiss index and writes it as
fasta format on STDOUT.
=head1 OPTIONS
-fmt <format> - Fasta (default), swiss or EMBL
-dir <dir> - directory where the index files are found
(overrides BIOPERL_INDEX environment variable)
Options for expert use
-type <db_type> - DBM_file type.
(overrides BIOPERL_INDEX_TYPE environment variable)
-v - report every index addition (debugging)
=head1 ENVIRONMENT
bp_index and bp_fetch coordinate where the databases lie using the
enviroment variable BIOPERL_INDEX. This can be overridden using the
-dir option. There is no default value, so you must use the -dir option
or set BIOPERL_INDEX.
The DB type is coordinated with BIOPERL_INDEX_TYPE which if it
is not there, defaults to whatever the bioperl modules have installed,
which itself defaults to SDBM_File.
=head1 USING IT YOURSELF
bp_index.pl is a script that drives the Index modules. If you want to
use this script heavily in your work, if it is Perl based, it is
almost certainly better to look at the code in this script and copy
it across (probably you will be more likely to want to use the bp_fetch
code).
=head1 EXTENDING IT
bp_index is just a wrapper around James Gilbert's excellent Index modules
found in bioperl
=head1 FEEDBACK
=head2 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
=head2 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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Ewan Birney
Ewan Birney E<lt>birney@ebi.ac.ukE<gt>
=cut
#'
use strict;
use warnings;
#
# Doofus catcher for people who are trying this script without
# installing bioperl
#
BEGIN {
eval {
require Bio::Index::Fasta;
require Bio::Index::EMBL;
require Bio::Index::Swissprot;
require Bio::Index::GenBank;
require Bio::Index::SwissPfam;
};
if ( $@ ) {
# one up from here is Bio directory - we hope!
push(@INC,"..");
eval {
require Bio::Index::Fasta;
require Bio::Index::EMBL;
};
if ( $@ ) {
print STDERR ("\nbp_index cannot find Bio::Index::Fasta and Bio::Index::EMBL\nbp_index needs to have bioperl installed for it to run.\nBioperl is very easy to install\nSee http://bio.perl.org for more information\n\n");
exit(1);
} else {
print STDERR ("\nYou are running bp_index.pl without installing bioperl.\nYou have done it from bioperl/scripts, and so we can find the necessary information\nbut it is much better to install bioperl\n\nPlease read the README in the bioperl distribution\n\n");
}
}
}
my $dir = $ENV{'BIOPERL_INDEX'};
my $type = $ENV{'BIOPERL_INDEX_TYPE'};
my $fmt = 'Fasta';
my $verbose = 0;
use Getopt::Long;
&GetOptions("f|fmt=s" => \$fmt,
"d|dir=s" => \$dir,
"t|type=s" => \$type,
"v!" => \$verbose);
exec('perldoc',$0) unless @ARGV;
my $name = shift;
if( !$dir ) {
print STDERR "\nNo directory specified for index\nDirectory must be specified by the environment varaible BIOPERL_INDEX or -dir option\ngo bp_index with no arguments for more help\n\n";
exit(1);
}
#
# Reset the type if needed
#
if( $type ) {
$Bio::Index::Abstract::USE_DBM_TYPE = $type;
}
#
# Rock and roll...
#
my $index;
$_ = $fmt;
SWITCH : {
/Fasta/i && do {
$index = Bio::Index::Fasta->new("$dir/$name", 'WRITE');
last;
};
/EMBL/i && do {
$index = Bio::Index::EMBL->new("$dir/$name", 'WRITE');
last;
};
/swisspfam|pfam/i && do {
$index = Bio::Index::SwissPfam->new("$dir/$name", 'WRITE');
last;
};
/swiss/i && do {
$index = Bio::Index::Swissprot->new("$dir/$name", 'WRITE');
last;
};
/GenBank/i && do {
$index = Bio::Index::GenBank->new("$dir/$name", 'WRITE');
last;
};
die("No index format called $fmt");
}
if( $verbose != 0 ) {
$index->verbose(1);
}
$index->make_index(@ARGV);
# finished. Neat eh.
#
# if you are using this in a script, to
# to force deallocation + closing of the index, go
# $index = undef;
#
|