The first 6 columns are always filled, the last two columns are only for some entries. So I have a main script that reads this file to process these ids further. I generally use
But how can I include the last two columns as well to run the command as many entries under the variable gene2 and gene3 are empty.
This is what i have tried so far to read all the lines in the file and if variable under gene2 and/or gene3 are empty, to move to the next line
I could do it for gene2 but wasnt able to implement it for gene3
This statement means that if there is no gene2 then there cannot be a gene3 read:
When you use the read statement you have to have all fields there in order to get gene3.
Otherwise gene3 is an "empty" variable. Or the same can happen for gene2.
You can create dummy values for those variables if they are empty, but since you have a separate script processing things that could affect the output of that script.
Try creating an intermediate file with dummy variables, let's use the word 'dummy' for the values of empties. This is awk, the output file will be called tmp.tmp which is what your script will have to use for input.
This could also be set up writing to a pipe which your existing script reads.
So the last 2 fields in tmp.tmp can be a real value, or just fiber filler: "dummy", but there will always be 8 fields. The last two fields cannot be blank or bash will not read them into a variable.
If you want to add a default/dummy within a bash script, you could do this:-
This says "assign the value of $my_var to itself, or the string default if it is empty or not set." You can have another variable instead of the string default if you want to.
Cope sample1: test.sh
i=0
echo " Outside loop i = $i "
while
do
i=$(( $i + 1))
echo "Inside loop i = $i "
done
echo " Out of loop i is : $i "
When run output :
Outside loop i = 0
Inside loop i = 1
Inside loop i = 2
Inside loop i = 3
Inside loop i = 4
Inside loop i = 5
Inside... (8 Replies)
Hi all,
Given here under a section of a script I am using.
SIMDIR="/home/Ins/forces"
cd $SIMDIR
for file in `ls *.forces`
do
basename=`echo $file | sed 's/\.*$//'`
extname=`echo $file | sed 's/*\(*\)\.\(.*\)/\2\1/'`
echo "Processing file: "$basename
python convert.py... (4 Replies)
I've a file in linux with following text:
;ip address hostname put-location alt-put-location tftpserver
192.168.1.1 r01-lab1-net /mnt/nas1/fgbu/ /opt/fgbu/devicebackup 192.168.1.254Now I want to read these values and assign them to particular variables... (6 Replies)
I have the following code and I am calling it using
./raytrac.bash -u
and getting problems. For some reason opt_usage is still 0.
opt_usage=0
iarg=0
narg=$#
while (($iarg < $narg))
do
(( iarg = $iarg + 1 ))
arg=$argv
usrInputFlag=`echo $arg | awk '/=/ {print 1}; ! /=/... (22 Replies)
I have a file that has four values on each line and I'd like to give each column a variable name and then use those values in each step of a loop. In bash, I believe you could use a while loop to do this or possibly a cat command, but I am super new to programming and I'm having trouble decoding... (2 Replies)
Hi All,
I am trying to read a .csv file which has some 6 columns.
Eg: samp.csv
one, two, three, four
six, seven, eight, nine
I used the following code,
for line in `cat samp.csv`
do
echo "$line"
done
It displays every comma seperated values in each line like,
one,... (1 Reply)
i get a name from user first name : last name, in this format. Now i am saving this to a file. what i want is, I do not want to save any name if I already have one entry o that same name..what should i do
for example
user give robert fernandez
this will save in file as robert:fernandez.
if... (5 Replies)
Hi.
I have the script shown below. If I execute it form the command line it seems to work properly, but when I fun it using the unix "at" command
"at -m now < ./kill-at-job.sh"
It appears to hang. Below is the script, the input file, and the execution as reported in the e-mail from the "at"... (3 Replies)
Hi,
I'm trying to write a script that reads filenames from a file and use these filenames in a loop. The filenames are all on one line and the problem is that these filenames have wildcards like * and braces like in them.
Right now what I'm doing is something like this:
echo "reading from... (0 Replies)
If no arguments are entered I wanna be able to read 2 arguments, i have done like this but it doesnt work:
x=0
until #loop starts
do
if ; then
echo No arguments were entered, please enter 2 arguments.
read $1 $2
elif || ; then
echo $#... (0 Replies)