Argthtjtr

I'm new to shell scripting, so i need all your help to achieve my goal. I have a file named input.csv which consists of data like shown below,

G22822 277 OR2

G22822 329 OR9

G22940 286 OR3

G22940 412 OR7

G25365 289 OR3

Now, OR2, OR9, OR3, OR7 and OR3 are also different files with the name as al_or2.cap, al_or9.cap, al_or3.cap, al_or7.cap and al_or3.cap in different path. The data present in these cap files are like shown below,

In al_or2.cap:

277 ASCII GRP 184578924

102 ASCII GRP 754815923

In al_or9.cap:

981 ASCII GRP 542189353

329 ASCII GRP 158203981

Like wise data present in all cap files.

If you see first line in input.csv(G22822 277 OR2) as data mentioned i need to go to al_or2.cap and search for keyword 277 and print G22822 and 542189353(G22822 present in input.csv and 542189353 present in al_or2.cap).

Then, for this G22822 329 OR9 i need to go to al_or9.cap and print G22822 and 158203981.

My required output like:

G22822 184578924

G22822 158203981 and so on..

Please help help me to achieve my goal.

Assuming that the data you presented is accurate, and not knowing your directory structure, here's a little something

#!/bin/bash

while read a b c

do

  awk -v a=$a -v b=$b  'b==$1{printf "%s %sn", a, $4}' tmp/al_$(echo $c | tr '[A-Z]' '[a-z]').cap

done < input.csv

Saving that as karthik.sh, having saved the first two lines of your input.csv, having created a subdirectory tmp with the files al_or2.cap and al_or9.cap in it, and running ./karthik.sh I get the following output:

./karthik.sh 

G22822 184578924

G22822 158203981

If your original file has 3-fields and your data files (e.g. al_or2.cap, etc..) all have 4-fields, you can use a single call to awk and the builtin functions tolower, sprintf, getline and split to form the filename, read the corresponding file and output the results in your desired order as follows:

awk '

{   lwr = tolower($3)

    str = sprintf ("al_%s.cap", lwr)

    while (getline line < str > 0) {

        split (line, a, " ", seps)

        if (a[1] == $2)

            print $1,a[4]

    }

}' file

Files Present

$ cat file

G22822 277 OR2

G22822 329 OR9

G22940 286 OR3

G22940 412 OR7

G25365 289 OR3



$ cat al_or2.cap

277 ASCII GRP 184578924

102 ASCII GRP 754815923



$ cat al_or9.cap

981 ASCII GRP 542189353

329 ASCII GRP 158203981

Example Use/Output

$ awk '

> {   lwr = tolower($3)

>     str = sprintf ("al_%s.cap", lwr)

>     while (getline line < str > 0) {

>         split (line, a, " ", seps)

>         if (a[1] == $2)

>             print $1,a[4]

>     }

> }' file

G22822 184578924

G22822 158203981

Creating a Simple awk Script

If you would like to create an awk-script from the above, you can do the following:

#!/usr/bin/awk -f

{

    lwr = tolower($3)

    str = sprintf ("al_%s.cap", lwr)

    while (getline line < str > 0) {

        split (line, a, " ", seps)

        if (a[1] == $2)

            print $1,a[4]

    }

}

Now all you need do is to save the file and make it executable (e.g. chmod +x myscript.awk, and then

Example Use/Output

$ ./myscript.awk file

G22822 184578924

G22822 158203981