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 SUSE
gst-complete
gst-complete-0.8(1) User Commands gst-complete-0.8(1)NAME
gst-complete-0.8, gst-complete - perform bash completion for gst-launch command lines
SYNOPSIS
complete -Cgst-complete-0.8 gst-launch
gst-complete [--gst-list-mm] [--gst-mm=string] [--print]
DESCRIPTION
gst-complete-0.8 enables bash to provide context-sensitive tab completion for gst-launch command lines. See gst-launch(1) for the syntax of
gst-launch command lines.
You must have a version of bash that supports programmable completion. Such versions of bash provide the complete built-in command.
gst-complete is a wrapper script that runs the latest installed version of gst-complete-X.X. For example, if both gst-complete-0.7 and gst-
complete-0.8 are installed on your system, gst-complete runs gst-complete-0.8.
OPTIONS
The following options are supported by gst-complete-0.8 and gst-complete:
--help Display detailed usage message. You can also use -? to specify this option.
The following options are supported by gst-complete only:
--gst-list-mm List found major/minor versions. This option displays the versions that are available.
--gst-mm=string Force major/minor version. This option enables you to specify a specific version to run, if you do not want to run the
default version.
--print Print wrapped command line. This option displays the command that will be run, and then runs the command.
EXAMPLES
Example 1: Generating the Registry of Available Plugins by Running gst-compprep
Run the following command in your .bash_profile or other appropriate place:
example% complete -C gst-complete-0.8 gst-launch
Example 2: Running the Wrapper Script and Displaying the Command Name
example% gst-complete --print
/usr/bin/gst-complete-0.8
FILES
The following files are used by this application:
/usr/bin/gst-complete-0.Executable for bash completion for gst-launch
/usr/bin/gst-complete Wrapper script that runs the latest installed version of gst-complete-X.X
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Availability |SUNWgnome-media |
+-----------------------------+-----------------------------+
|Interface stability |External |
+-----------------------------+-----------------------------+
SEE ALSO gst-compprep(1), gst-feedback(1), gst-inspect(1), gst-launch(1), gst-launch-ext(1), gst-md5sum(1), gst-register(1), gst-thumbnail(1), gst-
typefind(1), gst-xmlinspect(1), gst-xmllaunch(1), gstreamer-properties(1), libgstreamer-0.8(3), libgstgetbits(3)NOTES
Original man page written by the GStreamer team at http://gstreamer.net/.
Updated by Brian Cameron, Sun Microsystems Inc., 2004.
SunOS 5.10 14 Oct 2004 gst-complete-0.8(1)
07-30-2019
