Create a single bash script that does the following:
a. Print out the number of occurrences for each motif that is found in the bacterial genome and output to a file called motif_count.txt
b. Create a fasta file for each motif (so 3 in total) which contains all of the genes and their corresponding sequences that have that motif. Each file should be named after the motif (ie ATG.txt) and outputted to a new directory called motifs
motif file is a txt file with these motifs : ATG, GGGGG, ATTTT
the bacterial genome file is fasta file with the following lines
I have a very basic bash shell script, which has many "while... done; for .... done" loop clauses, like the following
~~
#!/bin/bash
while blablalba; do
....
done < /tmp/file
for line in `cat blablabla`; do grep $line /tmp/raw ; done > /tmp/1;
while blablalba2; do
....
done <... (2 Replies)
SEND_MESSAGE=test
echo $SEND_MESSAGE
if
then
echo `date` > update_dt_ccaps.lst
echo "The file transfer failed" >> update_dt_ccaps.lst
SEND_MESSAGE=false
fi
The above code is showing error in bash shell as :
./test: line 5: [: test: integer expression expected
... (2 Replies)
I'm trying to search all .odt files in a directory for a string in the text of the file.
I've found a bash script that works, except that it can't handle whitespace in the filenames.
#!/bin/bash
if ; then
echo "Usage: searchodt searchterm"
exit 1
fi
for file in $(ls *.odt); do
... (4 Replies)
Hi,
I am working on bash script after a long time. I am getting error near done statement while running a for loop snippet. The error says "Syntax error near unexpcted token 'done'"
please suggest what could be wrong. here is the snippet
elements=${#option_arr} //an array of values... (1 Reply)
Having issues with an expect script. I've been scripting bash, python, etc... for a couple years now, but just started to try and use Expect. Trying to create a script that takes in some arguments, and then for now, just runs a pwd command(for testing, final will be command I pass).
Here is... (0 Replies)
Hi Folks,
I have a loop that goes through an array and the output is funky.
sample:
array=( 19.239.211.30 )
for i in "${array}"
do
echo $i
iperf -c $i -P 10 -x CSV -f b -t 50 | awk 'END{print '$i',$6}' >> $file
done
Output:
19.239.211.30
19.2390.2110.3 8746886
seems that when... (2 Replies)
I have the following while loop that I put in a script, demo.sh:
while read rna; do
aawork=$(echo "${rna}" | sed -n -e 's/\(...\)\1 /gp' | sed -f rna.sed)
echo "$aawork" | sed 's/ //g'
echo "$aawork" | tr ' ' '\012' | sort | sed '/^$/d' | uniq -c | sed 's/*\(*\) \(.*\)/\2: \... (3 Replies)
Hi Everybody,
I'm a newbie to shell scripting, and I'd appreciate some help. I have a bunch of .txt files that have some unwanted content. I want to remove lines 1-3 and 1028-1098.
#!/bin/bash
for '*.txt' in <path to folder>
do
sed '1,3 d' "$f";
sed '1028,1098 d' "$f";
done
I... (2 Replies)
Dear all,
Please help with the following.
I have a file, let's call it data.txt, that has 3 columns and approx 700,000 lines, and looks like this:
rs1234 A C
rs1236 T G
rs2345 G T
Please use code tags as required by forum rules!
I have a second file, called reference.txt,... (1 Reply)
Hi everyone
I need some help
I want to create an script which does some processing
it takes the two arguments 201901010000 and 201901020200 - so YYYMMDDHHMM
I want to split processing into hours from start until end,
I dont get why this works but when I add to a future variable... (1 Reply)
Discussion started by: kl1ngac1k
1 Replies
LEARN ABOUT DEBIAN
xsil2graphics
XSIL2GRAPHICS(1) User Contributed Perl Documentation XSIL2GRAPHICS(1)NAME
xsil2graphics - generate scripts to load xsil output data files
SYNOPSIS
xsil2graphics [options] <xsil_file>
DESCRIPTION
Utility program bundled with xmds, used to generate scripts that load simulation output data into either matlab (http://www.mathworks.com)
or scilab (http://www.scilab.org), which are then used to manipulate the results further if necessary and then to present the results
graphically.
Matlab
To generate a matlab m-file, from the xsil file data_file.xsil use the command:
bash$ xsil2graphics data_file.xsil
or
bash$ xsil2graphics --matlab data_file.xsil
Then at the matlab command prompt:
>> data_file
Scilab
To generate a scilab script file, from the xsil file data_file.xsil use the command:
bash$ xsil2graphics --scilab data_file.xsil
Then at the scilab command prompt:
--> exec('data_file.sci')
OPTIONS -m, --matlab generate matlab m-file script to load data from the xsil data file (the default option)
-s, -scilab generate scilab script file to load data from the xsil data file
-o, --outfile <out_file> specify an alternative output script filename to the default which is the input xsil filename with the .xsil
extension changed to either .m for the matlab m-file or .sci for the scilab script file
EXAMPLES
bash$ xsil2graphics nlse.xsil
Generates the output nlse.m to load the data into matlab
bash$ xsil2graphics -m nlse.xsil
Also generates the output nlse.m but explicitly sets matlab to be the output format
bash$ xsil2graphics --scilab nlse.xsil
Generates the output nlse.sci to load the data into scilab
bash$ xsil2graphics --outfile nlse_new.m nlse.xsil
Generates the output nlse_new.m to load the data into matlab
AUTHORS
Originally written by Greg Collecutt
Maintained by Paul Cochrane with code contributed by Joe Hope
BUGS
No known bugs.
SEE ALSO xmds(1), loadxsil(1)
http://www.xmds.org
COPYRIGHT
Copyright (C) 2000-2004
Code contributed by Greg Collecutt, Joseph Hope and Paul Cochrane
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 2 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 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, write to the Free Software Foundation,
Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
perl v5.8.2 2004-06-21 XSIL2GRAPHICS(1)
07-30-2019
