hi,
i wat to get the output of a grep command in a file. but when i am trying out the same grep command in the unix prompt its working fine.. i am getting the output properly.. but when i am writing the same command inside my shell script , its just creating a new output file with no contents... (1 Reply)
I have a command nested in some while loops to parse some data that looks something like this.
while ($condition)
while ($condition)
...
gzcat /dir/$fileName.gz | grep $searchString > out_file
end
end
On the first loop, the command is executed properly (and takes maybe 10... (3 Replies)
here is a typical question for everyone ...
How to convert a given shell script to binaric command along with its shell script switches.
Any !dea (1 Reply)
Hi All,
Is there any way to monitor a command inside shell script ? I have a script inside which I have a tar command which zips around 200GB data.
tar zcvf $Bckp_Dir/$Box-BaseBackup-$Day.tar.gz * --exclude 'dbserver_logs/*' --exclude postmaster.pid --exclude 'pg_xlog/*'
I want to... (3 Replies)
Hi guys. Good day, morning, afternoon or night, depending on where you live.
I have a script shell in which I am looping on files (absolute path) see code section above.
I always have an error: bad substitution.
:wall:
Is it because my variable file is the index of the loop and not a normal... (4 Replies)
hii,,
I am trying to automate jira. during my scripting using bash script, in the terminal i got the terminal message like this:
"Configure which ports JIRA will use.
JIRA requires two TCP ports that are not being used by any other
applications on this machine. The HTTP port is where you... (1 Reply)
Hello Unix Shell Script Experts,
I have a script that would mask the columns in .csv file or .txt file.
First the script will untar the .zip files from Archive folder and processes into work folder and finally pushes the masked .csv files into Feed folder.
Two parameters are passed
... (5 Replies)
Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted!
1. The problem statement, all variables and given/known data:
This script will analyse the channels.txt e registrations.txt and it will allow to mage the channels and the... (9 Replies)
Discussion started by: Demas
9 Replies
LEARN ABOUT DEBIAN
proftmb
PROFTMB(1) User Commands PROFTMB(1)NAME
proftmb - per-residue prediction of bacterial transmembrane beta barrels
SYNOPSIS
proftmb [options]
DESCRIPTION
proftmb predicts bacterial transmembrane beta barrels from sequence using profile fed Hidden Markov Models (HMM).
Output format
Self-annotating. Letters of prediction: 'i' - inside cytoplasm, 'O' - outside cytoplasm, 'U' - up (on chain moving out of cytoplasm), 'D'
- down (on chain moving into cytoplasm).
References
Bigelow, H. and Rost, B. (2006). PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res,
34(Web Server issue), W186-8.
To invoke the menu, type:
proftmb --menu
The options are:
-d, --directory-root <STRING>
root path where files (options -s,-r,-l,-a,-e,-t,-u,-z,-n) reside
-a, --reduction-state-decode <STRING>
state reduction for decoding
-b, --reduction-state-report <STRING>
state reduction for reporting
-m, --membrane-strand-states <STRING>
list of membrane strand states
-z, --z-curve-file
<STRING> file containing means and sd's at integral length values
-x, --z-calibration-curve <STRING>
file mapping coverage and accuracy values to z-scores
-n, --null-frequency <STRING>
background frequency file
-c, --minimum-score-cutoff <DOUBLE>
minimum z-score for per-residue prediction
-o, --outfile-prefix <STRING>
output file prefix for the three files generated: PREFIX_dat.txt, PREFIX_proftmb_pretty.txt PREFIX_proftmb_tabular.txt
-s, --static-model-data <STRING>
data representing the model architecture
-t, --trained-params <STRING>
params representing the encoded training data
-q, --test-blastQ-file-or-dir <STRING>
psiblast profile (-Q) or directory (full pathname or relative to current directory) with many profiles
-w, --single-sequence-name <STRING>
if -q option points to a single file, this is the name
-v, --list-blastQ-files <STRING>
list of psiblast files to process in directory (leave blank to process all files)
--outfile-pretty <STRING>
pretty output file (overrides automatic name PREFIX_proftmb_pretty.txt)
--outfile-tab
<STRING> tabulated output file (overrides automatic name PREFIX_proftmb_tabular.txt)
--outfile-dat
<STRING> data output file (overrides automatic name PREFIX_dat.txt)
--version
<BOOL> output version information and exit
--quiet
<BOOL> be quiet
EXAMPLES
proftmb @/usr/share/proftmb/options -q /usr/share/doc/proftmb/examples/example.Q -o /tmp/example
The above produces 3 output files: /tmp/example_proftmb_tabular.txt, /tmp/example_proftmb_pretty.txt and /tmp/example_dat.txt. Compare
these to the examples in /usr/share/doc/proftmb/examples.
BUGS
Please report bugs at <https://rostlab.org/bugzilla3/enter_bug.cgi?product=proftmb>.
COPYRIGHT
Copyright (C) 2004 Henry Bigelow
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 package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MER-
CHANTABILITY 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/>.
proftmb 1.1.10 February 2012 PROFTMB(1)