reprof(1) [debian man page]
REPROF(1) User Commands REPROF(1) NAME
reprof - predict protein secondary structure and solvent accessibility SYNOPSIS
reprof -i [query.blastPsiMat] [OPTIONS] reprof -i [query.fasta] [OPTIONS] reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [OPTIONS] DESCRIPTION
Predict protein secondary structure and solvent accessibility. Output Format The output format is self-explanatory, i.e. the colums of the output are described in the output file itself. OPTIONS
-i, --input=FILE Input BLAST PSSM matrix file (from Blast -Q option) or input (single) FASTA file. -o, --out=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. --mutations=[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. --modeldir=DIR Directory where the model and feature files are stored. Default: /usr/share/reprof. AUTHOR
Peter Hoenigschmid hoenigschmid@rostlab.org, Burkhard Rost EXAMPLES
Prediction from BLAST PSSM matrix for best results: reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof Prediction from FASTA file: reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof 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. 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/>. BUGS
https://rostlab.org/bugzilla3/enter_bug.cgi?product=reprof SEE ALSO
blast2(1) http://rostlab.org/ 1.0.1 2012-01-13 REPROF(1)
Check Out this Related Man Page
COMP_ERR(1) MySQL Database System COMP_ERR(1) NAME
comp_err - compile MySQL error message file SYNOPSIS
comp_err [options] DESCRIPTION
comp_err creates the errmsg.sys file that is used by mysqld to determine the error messages to display for different error codes. comp_err normally is run automatically when MySQL is built. It compiles the errmsg.sys file from the plaintext file located at sql/share/errmsg.txt in MySQL source distributions. comp_err also generates mysqld_error.h, mysqld_ername.h, and sql_state.h header files. For more information about how error messages are defined, see the MySQL Internals Manual[1]. Invoke comp_err like this: shell> comp_err [options] comp_err supports the following options. o --help, -? Display a help message and exit. o --charset=path, -C path The character set directory. The default is ../sql/share/charsets. o --debug=debug_options, -# debug_options Write a debugging log. A typical debug_options string is d:t:O,file_name. The default is d:t:O,/tmp/comp_err.trace. o --debug-info, -T Print some debugging information when the program exits. o --header_file=file_name, -H file_name The name of the error header file. The default is mysqld_error.h. o --in_file=file_name, -F file_name The name of the input file. The default is ../sql/share/errmsg.txt. o --name_file=file_name, -N file_name The name of the error name file. The default is mysqld_ername.h. o --out_dir=path, -D path The name of the output base directory. The default is ../sql/share/. o --out_file=file_name, -O file_name The name of the output file. The default is errmsg.sys. o --statefile=file_name, -S file_name The name for the SQLSTATE header file. The default is sql_state.h. o --version, -V Display version information and exit. COPYRIGHT
Copyright (C) 1997, 2014, Oracle and/or its affiliates. All rights reserved. This documentation is free software; you can redistribute it and/or modify it only under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License. This documentation 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 the program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA or see http://www.gnu.org/licenses/. NOTES
1. MySQL Internals Manual http://dev.mysql.com/doc/internals/en SEE ALSO
For more information, please refer to the MySQL Reference Manual, which may already be installed locally and which is also available online at http://dev.mysql.com/doc/. AUTHOR
Oracle Corporation (http://dev.mysql.com/). MySQL 5.5 01/30/2014 COMP_ERR(1)