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Top Forums Shell Programming and Scripting inserting and replacing lines with awk Post 302530013 by tempestas on Sunday 12th of June 2011 07:22:29 AM
Old 06-12-2011
Hi,

sorry, I thought the longer examples help to better understand the structure, because the input files are a mess, but they are given to me like that.
I shortened the examples in my former posts. I hope now it becomes more clear what I wanna do.

Thanks a lot!

tempestas
 

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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)
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