In the bash menu below if the variant that is inputted is in the format NM_004004.3:c.274G>T the below works perfectly. My question is if the variant inputted isNM_004004.3:-c.274G>T or NM_004004.3:+c.274G>T then the code as is will throw an error due to a biological issue. Is it possible to to have variants that have either a -/+ in them skip the additional function and go straight to the nomenclature function? I apologize for any confusion I am not sure how to explain this, but basically if variants with a -/+ in them go to the additional function then they will error. I don't know if there can be a special case coded in or if there is a better way. Thank you .
Hello,
Today, as a root user, i want to copy recursively all files and diretories in a source directory to a destination directory using the following command,
cp -r /home/smith/* /home/bob/
However, I carelessly missed the '*' out when I executed the command.
Now, i noticed a... (1 Reply)
Hi Gurus,
I had a question regarding avoiding duplicates.i have a file abc.txt
abc.txt
-------
READER_1_1_1> HIER_28056 XML Reader: Error occurred while parsing:; line number ; column number
READER_1_3_1> Sun Mar 23 23:52:48 2008
READER_1_3_1> HIER_28056 XML Reader: Error occurred while... (0 Replies)
Below is my menu options code. It allows user to pick one of two option. I can get the first option to work, because if it is selected it just "breaks" and carries on with the script.
What i want to know is if a user selects option two how do i get that option to ignore all the other script and... (6 Replies)
hello all
i have a big problems for me
if i have more files as example
test.ghrt.part01.rar
test.ghrt.part02.rar
test.ghrt.part03.rar
test.ghrt.part04.rar
test.ghrt.part05.rar
test.ghrt.part06.rar
test.ghrt.part07.rar
test.ghrt.part08.rar
test.ghrt.part09.rar
test.ghrt.part10.rar... (13 Replies)
the idea is to create script with menu and when option 1 or2 is pressed program should clear screan display info and get back to menu....
I managed some code but getting errors...
#!/bin/bash
choice1=ls -l|awk'{print $9 $1}'
choice2= ls | wc -c
choice3=exit
while
do
clear
echo "... (8 Replies)
EDIT : System used : Any Linux distribution.
Hello everyone,
I m having quite a headache trying to figure out why I m having a 2 columns output in the following code :
#!/bin/ksh
menu_rotation()
{
#Variables
CHOIX1="Rotation 1"
CHOIX2="Rotation 2"
CHOIX3="Rotation 3"
... (11 Replies)
hi all i am a newbie to this
is there any examples on creating a main menu with 3 sub menu
main menu -> option a , b and c
a menu -> option 1 ,2 and 3
b menu -> option 1 ,2
c menu -> option 1 ,2
i am getting headache as my code kept getting unexpected EOF
---------- Post... (0 Replies)
hi all
i am trying to get help with writing a script using case statement to display menu as
1) Authentication log
2) System log
3) Messages
4) Dmesg
5) Boot log
Q) Exit
When selecting the menu by 1 or 2 or 3 o 4 or 5, it should display the last 10 lines of the log files,
if... (3 Replies)
I have a special case that awk could be used but I do not have the skill. Trying to create a final output file (indel_parse.txt) that is created from using some information from each of the two files (attached).
parse rules:
The header is skipped FNR>1
1. 4 zeros after the NC_ (not... (2 Replies)
Hello,
I have a question regarding while loop and existence of files.
I am running under ubuntu 18.04 bionic, have around fifty video files inside the directory.
script:
for file in *.mp4
do
/root/bin/ffmpeg -i $file \
-i $(basename "${file/.mp4}").bs.srt \
-i $(basename... (12 Replies)
Discussion started by: baris35
12 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)