Bash Programming

Question

I've been trying all the morning thinking how to do what I want to do but... I am starting to feel desperate!

I have an array of rows and columns in a .txt file. So I want to create a script that gives to me this information:

If I type it to the terminal (script.sh 1 2 3), it should give me columns 1 to 3 from the .txt file.

If I type it to the terminal (script.sh), it should give me column 5 to the last column.

If I type it to the terminal (script.sh 1 2 3 -g insulin), it should give me columns 1 to 3 of the rows that contain the word "insulin". The -g here means "gene", so the aim is to look for that gene.

I've written a code that gives me the columns I want or all the columns if I don't introduce any variable, but I can't go ahead with the -g and gene variables... Do you have any idea?

Here's my code:

#!/bin/bash

var="$(echo $@ | tr " " ",")"

if [ $# = 0 ]; then
awk '{for (x=5; x<=NF; x++) {printf "%s ", $x } printf "\n" }' affy.txt
else
cat affy.txt | cut -d" " -f$var
fi

Thank you!

glenn jackman · Accepted Answer · 2013-10-16 15:30:24Z

2

script.sh:

#!/bin/bash
columns=""
word="."
for arg; do
    if [[ $arg == "-g" ]]; then
        shift
        word=$1
    else
        columns+="$1,"
    fi
    shift
done
if [[ $columns ]]; then
    columns=${columns%,}
else
    columns="5-"
fi
grep $word affy.txt | cut -d " " -f "$columns"

edited Oct 16, 2013 at 15:30

answered Oct 16, 2013 at 15:24

glenn jackman

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1 Comment

sofly Over a year ago

nice use of shift to parse the args

cxw · Accepted Answer · 2013-10-16 13:39:47Z

0

You want your awk script to know about the search string from -g. To pass values into a script, I have had good success with the -v argument of gawk. Once you have the argument of -g in your script in variable lookfor (e.g., using getopt), run:

 gawk -v searchtext="$lookfor" -- '$0 ~ searchtext { print $1, $2, $3 }'

The -v argument makes searchtext refer to $lookfor, i.e., the argument to -g in the bash script. Then $0 ~ searchtext selects any line where the search text is anywhere on the line. For matching lines, the first three fields are printed.

answered Oct 16, 2013 at 13:39

cxw

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