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 CENTOS
pmdabash
PMDABASH(1) General Commands Manual PMDABASH(1)NAME
pmdabash - Bourne-Again SHell trace performance metrics domain agent
SYNOPSIS
$PCP_PMDAS_DIR/bash/pmdabash [-C] [-d domain] [-l logfile] [-I interval] [-t timeout] [-U username] configfile
DESCRIPTION
pmdabash is an experimental Performance Metrics Domain Agent (PMDA) which exports "xtrace" events from a traced bash(1) process. This
includes the command execution information that would usually be sent to standard error with the set -x option to the shell.
Event metrics are exported showing each command executed, the function name and line number in the script, and a timestamp. Additionally,
the process identifier for the shell and its parent process are exported.
This requires bash version 4 or later.
A brief description of the pmdabash command line options follows:
-d It is absolutely crucial that the performance metrics domain number specified here is unique and consistent. That is, domain should
be different for every PMDA on the one host, and the same domain number should be used for the same PMDA on all hosts.
-l Location of the log file. By default, a log file named bash.log is written in the current directory of pmcd(1) when pmdabash is
started, i.e. $PCP_LOG_DIR/pmcd. If the log file cannot be created or is not writable, output is written to the standard error
instead.
-s Amount of time (in seconds) between subsequent evaluations of the shell trace file descriptor(s). The default is 2 seconds.
-m Maximum amount of memory to be allowed for each event queue (one per traced process). The default is 2 megabytes.
-U User account under which to run the agent. The default is the unprivileged "pcp" account in current versions of PCP, but in older
versions the superuser account ("root") was used by default.
INSTALLATION
In order for a host to export the names, help text and values for the bash performance metrics, do the following as root:
# cd $PCP_PMDAS_DIR/bash
# ./Install
As soon as an instrumented shell script (see INSTRUMENTATION selection below) is run, with tracing enabled, new metric values will appear -
no further setup of the agent is required.
If you want to undo the installation, do the following as root:
# cd $PCP_PMDAS_DIR/bash
# ./Remove
pmdabash is launched by pmcd(1) and should never be executed directly. The Install and Remove scripts notify pmcd(1) when the agent is
installed or removed.
INSTRUMENTATION
In order to allow the flow of event data between a bash(1) script and pmdabash, the script should take the following actions:
#!/bin/sh
source $PCP_DIR/etc/pcp.sh
pcp_trace on $@ # enable tracing
echo "awoke, $count"
pcp_trace off # disable tracing
The tracing can be enabled and disabled any number of times by the script. On successful installation of the agent, several metrics will
be available:
$ pminfo bash
bash.xtrace.numclients
bash.xtrace.maxmem
bash.xtrace.queuemem
bash.xtrace.count
bash.xtrace.records
bash.xtrace.parameters.pid
bash.xtrace.parameters.parent
bash.xtrace.parameters.lineno
bash.xtrace.parameters.function
bash.xtrace.parameters.command
When an instrumented script is running, the generation of event records can be verified using the pmevent(1) command, as follows:
$ pmevent -t 1 -x '' bash.xtrace.records
host: localhost
samples: all
bash.xtrace.records["4538 ./test-trace.sh 1 2 3"]: 5 event records
10:00:05.000 --- event record [0] flags 0x19 (point,id,parent) ---
bash.xtrace.parameters.pid 4538
bash.xtrace.parameters.parent 4432
bash.xtrace.parameters.lineno 43
bash.xtrace.parameters.command "true"
10:00:05.000 --- event record [1] flags 0x19 (point,id,parent) ---
bash.xtrace.parameters.pid 4538
bash.xtrace.parameters.parent 4432
bash.xtrace.parameters.lineno 45
bash.xtrace.parameters.command "(( count++ ))"
10:00:05.000 --- event record [2] flags 0x19 (point,id,parent) ---
bash.xtrace.parameters.pid 4538
bash.xtrace.parameters.parent 4432
bash.xtrace.parameters.lineno 46
bash.xtrace.parameters.command "echo 'awoke, 3'"
10:00:05.000 --- event record [3] flags 0x19 (point,id,parent) ---
bash.xtrace.parameters.pid 4538
bash.xtrace.parameters.parent 4432
bash.xtrace.parameters.lineno 47
bash.xtrace.parameters.command "tired 2"
10:00:05.000 --- event record [4] flags 0x19 (point,id,parent) ---
bash.xtrace.parameters.pid 4538
bash.xtrace.parameters.parent 4432
bash.xtrace.parameters.lineno 38
bash.xtrace.parameters.function "tired"
bash.xtrace.parameters.command "sleep 2"
FILES
$PCP_PMCDCONF_PATH
command line options used to launch pmdabash
$PCP_PMDAS_DIR/bash/help
default help text file for the bash metrics
$PCP_PMDAS_DIR/bash/Install
installation script for the pmdabash agent
$PCP_PMDAS_DIR/bash/Remove
undo installation script for pmdabash
$PCP_LOG_DIR/pmcd/bash.log
default log file for error messages and other information from pmdabash
PCP ENVIRONMENT
Environment variables with the prefix PCP_ are used to parameterize the file and directory names used by PCP. On each installation, the
file /etc/pcp.conf contains the local values for these variables. The $PCP_CONF variable may be used to specify an alternative configura-
tion file, as described in pcp.conf(5).
SEE ALSO bash(1), pmevent(1) and pmcd(1).
Performance Co-Pilot PCP PMDABASH(1)
07-30-2019
