I have a groups of files in a folder. Each group is identified by characters 3-6 in the file name. I want to read in all the files of the group, count how many files there are, and then assign the file name to a variable made up of some letters and the counter. e.g. FILENAME$COUNTER. My code is almost working but there seems to be a problem with assigning the counter to the variable name.
I get this error for the line with code FILE$COUNTER=$i
line 12: FILE1=5_lib1ln1_BWA_ddrot_testonl_pe12.bam: command not found
This is exactly what I wanted for the variable name and assignment, but its saying command not found. I'm not sure why there is a command not found.
#!/bin/bash
## All files from the same group have the same LIB
LIB='lib1'
COUNTER=0
for i in 5_*.bam
do
SAMPLIB=`echo $i | cut -c 3-6`
if [ "$LIB" = "$SAMPLIB" ]; then
let COUNTER++
FILE$COUNTER=$i
fi
NUMFILES=$COUNTER
done
Replace
FILE$COUNTER=$i
with
eval FILE$COUNTER=$i
See eval command in Bash and its typical uses for more information.
Related
I'm trying to write a simple script that creates five textfiles enumerated by a variable in a loop. Can anybody tell my how to make the arithmetic expression be evaluated. This doesn't seem to work:
touch ~/test$(($i+1)).txt
(I am aware that I could evaluate the expression in a separate statement or change of the loop...)
Thanks in advance!
The correct answer would depend on the shell you're using. It looks a little like bash, but I don't want to make too many assumptions.
The command you list touch ~/test$(($i+1)).txt will correctly touch the file with whatever $i+1 is, but what it's not doing, is changing the value of $i.
What it seems to me like you want to do is:
Find the largest value of n amongst the files named testn.txt where n is a number larger than 0
Increment the number as m.
touch (or otherwise output) to a new file named testm.txt where m is the incremented number.
Using techniques listed here you could strip the parts of the filename to build the value you wanted.
Assume the following was in a file named "touchup.sh":
#!/bin/bash
# first param is the basename of the file (e.g. "~/test")
# second param is the extension of the file (e.g. ".txt")
# assume the files are named so that we can locate via $1*$2 (test*.txt)
largest=0
for candidate in (ls $1*$2); do
intermed=${candidate#$1*}
final=${intermed%%$2}
# don't want to assume that the files are in any specific order by ls
if [[ $final -gt $largest ]]; then
largest=$final
fi
done
# Now, increment and output.
largest=$(($largest+1))
touch $1$largest$2
this is my first stackoverflow question, regarding bash scripting. I am a beginner in this language, so be kind with me.
I am trying to write a comparison script. I tried to store all the outputs into variables, but only the last one is stored.
Example code:
me:1234567
you:2345678
us:3456789
My code:
#!bin/bash
while read -r forName forNumber
do
aName="$forName"
echo "$aName"
aNumber="$forNumber"
echo "$aNumber"
done < "exampleCodeFile.txt"
echo "$aNumber"
For the first time, everything will be printed out fine. However, the second echo will only print out "3456789", but not all the numbers again. Same with $aName. This is a problem because i have another file, which i stored a bunch of numbers to compare $aNumber with, using the same method listed above, called $aMatcher, consisting:
aMatcher:
1234567
2345678
3456789
So if i tried to run a comparison:
if [ "$aNumber" == "$aMatcher" ]; then
echo "match found!"
fi
Expected output (with bash -x "scriptname"):
'['1234567 == 1234567']'
echo "match found!"
Actual output (with bash -x "scriptname"):
'['3456789 == 3456789']'
echo "match found!"
Of course my end product would wish to list out all the matches, but i wish to solve my current issue before attempting anything else. Thanks!
When you run your following code
aNumber="$forNumber"
You are over-writing the variable $aNumber for every line of the file exampleCodeFile.txt rather than appending.
If you really want the values to be appended, change the above line to
aNumber="$aNumber $forNumber"
And while matching with $aMatcher, you again have to use a for/while loop to iterate through every value in $aNumber and $aMatcher.
I am trying to write a bash script which allows me to automate the creation of multiple directories with incrementing names.
For example, I am trying to create the directories named v0v1, v1v2, ... , v40v41.
I have tried using a 'for' loop, where I create a variable and set this to be equal to the current value of i+1 (where 'i' is the current loop iteration), but it is not working as expected.
I have managed to get the variable to increment (and have checked this using 'echo'), but I cannot get it to become part of the new directory name.
The code I have written is as follows:
for i in {0..40}; do let r=$((i+1)); mkdir v$iv$r; done
However, the directories produced have names only containing the first variable value (i.e. v0, v1, ..., v40), and do not include the 'v$r' at all.
Does anyone have any ideas how to use two variables at once in the same filename?
printf 'r=%d ; mkdir v$((r-1))v${r} ;' $(seq 2 41) |sh
You don't need a shell loop at all.
for i in {0..40}; do let r=$((i+1)); mkdir v${i}v$r; done
When bash sees the expression v$iv$r, it substitutes in for variables iv and r. But, of course, there is no iv. So bash substitutes in the empty string. The solution is to use braces to assure that bash knows where the variable name ends. Thus: v${i}v$r.
I've got a bash script accepting several files as input which are mixed with various script's options, for example:
bristat -p log1.log -m lo2.log log3.log -u
I created an array where i save all the index where i can find files in the script's call, so in this case it would be an arrat of 3 elements where
arr_pos[0] = 2
arr_pos[1] = 4
arr_pos[3] = 5
Later in the script I must call "head" and "grep" in those files and i tried this way
head -n 1 ${arr_pos[0]}
but i get this error non runtime
head: cannot open `2' for reading: No such file or directory
I tried various parenthesis combinations, but I can't find which one is correct.
The problem here is that ${arr_pos[0]} stores the index in which you have the file name, not the file name itself -- so you can't simply head it. The array storing your arguments is given by $#.
A possible way to access the data you want is:
#! /bin/bash
declare -a arr_pos=(2 4 5)
echo ${#:${arr_pos[0]}:1}
Output:
log1.log
The expansion ${#:${arr_pos[0]}:1} means you're taking the values ranging from the index ${arr_pos[0]} in the array $#, to the element of index ${arr_pos[0]} + 1 in the same array $#.
Another way to do so, as pointed by #flaschenpost, is to eval the index preceded by $, so that you'd be accessing the array of arguments. Although it works very well, it may be risky depending on who is going to run your script -- as they may add commands in the argument line.
Anyway, you may should try to loop through the entire array of arguments by the beginning of the script, hashing the values you find, so that you won't be in trouble while trying to fetch each value later. You may loop, using a for + case ... esac, and store the values in associative arrays.
I think eval is what you need.
#!/bin/bash
arr_pos[0]=2;
arr_pos[1]=4;
arr_pos[2]=5;
eval "cat \$${arr_pos[1]}"
For me that works.
I have one loop that creates a group of variables like DISK1, DISK2... where the number at the end of the variable name gets created by the loop and then loaded with a path to a device name. Now I want to use those variables in another loop to execute a shell command, but the variable doesn't give its contents to the shell command.
for (( counter=1 ; counter<=devcount ; counter++))
do
TEMP="\$DISK$counter"
# $TEMP should hold the variable name of the disk, which holds the device name
# TEMP was only for testing, but still has same problem as $DISK$counter
eval echo $TEMP #This echos correctly
STATD$counter=$(eval "smartctl -H -l error \$DISK$counter" | grep -v "5.41" | grep -v "Joe")
eval echo \$STATD$counter
done
Don't use eval ever, except maybe if there is no other way AND you really know what you are doing.
The STATD$counter=$(...) should give an error. That's not a valid assignment because the string "STATD$counter" is not a valid variable name. What will happen is (using a concrete example, if counter happened to be 3 and your pipeline in the $( ) output "output", bash will only expand that line as far as "STATD3=output" so it will try to find a command named "STATD3=output" and run it. Odds are this is not what you intended.
It sounds like everything you want to do can be accomplished with arrays instead. If you are not familiar with bash arrays take a look at Greg's Wiki, in particular this page or the bash man page to find out how to use them.
For example, in the loop you didn't post in your question: make disk (not DISK: don't use all upper case variable names) an array like so
disk+=( "new value" )
or even
disk[counter]="new value"
Then in the loop in your question, you can make statd an array as well and assign it with values from disk by
statd[counter]="... ${disk[counter]} ..."
It's worth saying again: avoid using eval.