passing command line arguments to awk in shell script

Question

Background information:

I am trying to write a small shell script, which searches a pattern (string) in a .fas-file and prints the line and position, where the pattern was found. The following code snippet works, when I call the shell script:

Script (search.sh):

#!/bin/bash

awk 's=index($0, "CAATCTCC"){print "line=" NR, "start position=" s}' 100nt_upstream_of_mTSS.fas

Command line call:

$ ./search.sh

First problem:

When I change the script to:

awk 's=index($0, "CAATCTCC"){print "line=" NR, "start position=" s}'

and do the following command line call in my bash:

$ ./search.sh 100nt_upstream_of_mTSS.fas

"nothing" happens (something is running, but it takes way too long and no results come up, so terminate the process).

Worth to know:

I am in the directory, where search.sh is located
the file 100nt_upstream_of_mTSS.fas is located there, too
search.sh is executable

I might be "screen blind", but I can't find the reason, why I am unable to pass a command line argument to my script.

Solution - see comments

Note: Only the first occurence of the pattern in a line is found this way.

Second problem:

Furthermore, I would like to make the motif (the string) I search for variable. I tried this:

Script:

#!/bin/bash
FILE=$1
MOTIF=$2
awk 's=index($0, "$MOTIF"){print "line=" NR, "start position=" s}' "$FILE"

Command line call:

$ ./search.sh 100nt_upstream_of_mTSS.fas CAATCTCC

Idea: First command-line argument worked and was substitued correctly. Why is the second one not substituted correctly?

Solution so far:

Script:

#!/bin/bash
file=$1
awk -v s="$2" 'i=index($0, s){print "line: " NR, "pos: " i}' "$file"

Testing:

Testfile (test.txt):

1 GAGAGAGAGA

2 CTCTCTCTCT

3 TATATATATA

4 CGCGCGCGCG

5 CCCCCCCCCC

6 GGGGGGGGGG

7 AAAAAAAAAA

8 TTTTTTTTTT

9 TGATTTTTTT

10 CCCCCCCCGA

 $ ./search.sh test.txt GA

will print:

line: 1 pos: 1

line: 4 pos: 2

line: 6 pos: 1

line: 9 pos: 2

line: 10 pos: 9

This script will print line and first match position in the line of only the first character of my pattern. How do I manage to have all results printed and the full pattern being used?

RavinderSingh13 · Accepted Answer · 2017-10-22 09:09:19Z

2

As far as I understood you want to pass the Input_file(file which you want to process by script) as an argument, if this is the case then following may help you in same.

cat search.sh
#!/bin/bash
variable=$1
awk 's=index($0, "CAATCTCC"){print "line=" NR, "start position=" s}' "$variable"

./search.sh 100nt_upstream_of_mTSS.fas

answered Oct 22, 2017 at 9:09

RavinderSingh13

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1 Comment

Shushiro Over a year ago

Yes, this helped! So, awk needs the variable parameter in the end, and I missed that? I feel like I did not fully understand the awk structure yet, but I will do some more research.

Collectives™ on Stack Overflow

passing command line arguments to awk in shell script

Background information:

Script (search.sh):

Command line call:

First problem:

Worth to know:

Solution - see comments

Note: Only the first occurence of the pattern in a line is found this way.

Second problem:

Script:

Command line call:

Solution so far:

Script:

Testing:

1 Answer 1

1 Comment

Your Answer

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Collectives™ on Stack Overflow

Background information:

Script (search.sh):

Command line call:

First problem:

Worth to know:

Solution - see comments

Note: Only the first occurence of the pattern in a line is found this way.

Second problem:

Script:

Command line call:

Solution so far:

Script:

Testing:

1 Answer 1

1 Comment

Your Answer

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