/usr/bin/reprof is in reprof 1.0.1-1.
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 | #!/usr/bin/perl
#--------------------------------------------------
# Predict secondary structure and solvent
# accessibility from sequece
#
# Author: hoenigschmid@rostlab.org
#--------------------------------------------------
use strict;
use warnings;
use Carp;
use Getopt::Long;
use Cwd;
use Pod::Usage;
use RG::Reprof;
# popularity contest
if( system('pp_popcon_cnt', '-p', 'reprof') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); }
# Parameters
my $input_file;
my $out_file;
my $mutation_file;
my %specific_models;
my $model_dir = "/usr/share/reprof";
if (! -e $model_dir) {
$model_dir = "/mnt/project/reprof/share/";
}
GetOptions(
"input=s" => \$input_file,
"out=s" => \$out_file,
"modeldir=s" => \$model_dir,
"mutations=s" => \$mutation_file,
"spec=s" => \%specific_models,
);
# Check if either blastPsiMat or fasta file is present
if( !defined $input_file || !-e $input_file ){ pod2usage(-verbose => 1); }
my $reprof = RG::Reprof::Reprof->new( model_dir => $model_dir );
my $ret = $reprof->run( input_file => $input_file, out_file => $out_file, mutation_file => $mutation_file, specific_models => \%specific_models );
exit $ret;
__END__
=head1 NAME
reprof - predict protein secondary structure and solvent accessibility
=head1 SYNOPSIS
reprof -i [query.blastPsiMat] [OPTIONS]
reprof -i [query.fasta] [OPTIONS]
reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [OPTIONS]
=head1 DESCRIPTION
Predict protein secondary structure and solvent accessibility.
=head2 Output Format
The output format is self-explanatory, i.e. the colums of the output are described in the output file itself.
=head1 OPTIONS
=over
=item B<-i, --input>=I<FILE>
Input BLAST PSSM matrix file (from Blast -Q option) or input (single) FASTA file.
=item B<-o, --out>=I<FILE>
Either an output file or a directory. If not provided or a directory, the suffix of the input filename (i.e. .fasta or .blastPsiMat) is replaced to create an output filename.
=item B<--mutations>=I<[all|FILE]>
Either the keyword "all" to predict all possible mutations or a file containing mutations one per line such as "C12M" for C is mutated to M on position 12:
C30Y
R31W
G48D
This mutation code is also attached to the output filename using "_".
An additional file ending "_ORI" contains the prediction using no evolutionary information even if a BLAST PSSM matrix was provided.
=item B<--modeldir>=I<DIR>
Directory where the model and feature files are stored. Default: F</usr/share/reprof>.
=back
=head1 AUTHOR
Peter Hoenigschmid L<hoenigschmid@rostlab.org>, Burkhard Rost
=head1 EXAMPLES
=over
=item Prediction from BLAST PSSM matrix for best results:
reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof
=item Prediction from FASTA file:
reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof
=item Prediction from BLAST PSSM matrix file using the mutation mode:
reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/mutations_example.Q.reprof --mutations /usr/share/doc/reprof/examples/mutations.txt
# Result files for the above call are going to be:
# /tmp/mutations_example.Q.{reprof,reprof_F172P,reprof_M1Q,reprof_N34Y,reprof_ORI} - see --mutations for a description of the extensions.
=back
=head1 COPYRIGHT
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 3 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, see <http://www.gnu.org/licenses/>.
=head1 BUGS
https://rostlab.org/bugzilla3/enter_bug.cgi?product=reprof
=head1 SEE ALSO
blast2(1)
http://rostlab.org/
=cut
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