Shell Programming and Scripting

Hello experts,

It has been just one month since I started with perl. I have the following doubt.

I have two files

File 1 looks like this

Code:

GKHGGSS0098       PPP.100.F.LE
GKHYXDF9081       KKK.100.F.LE
GKHSDFT6546       JKL.100.F.LE
GKHGGHJ3123       ABC.100.F.LE

File 2 looks like this

Code:

>GKHGGSS0098 
atatatatagacagatgaacagat
>GKHGGSS0098 
atatatatatatatatatatatatatatata
>GKHYXDF9081
gggacacatagacagatagaca
>GKHSDFT6546
gacagatatatatatatatatata
>GKHGGHJ3123
ggccgcgcgcatagacaccagatagacagat

So I want to write a script that reads column 2 in file 1 and considers only those entries whose first 3 letters are PPP or KKK.

In the above there is one PPP and one KKK so the script will take two entries from the file. The the script needs to see the first column value for PPP and KKK, which are GKHGGSS0098 and GKHYXDF9081.

Finally the script will compare these first column values of file one with that of file two (with the part after the > sign).

Once they match, the script will extract them from file two and store them in a result file.

So in this case, the output file will have

Code:

>GKHGGSS0098 
atatatatagacagatgaacagat
>GKHGGSS0098 
 atatatatatatatatatatatatatatata
>GKHYXDF9081
gggacacatagacagatagaca

I donot know how to go about with this. Should I use a hash. Please help

Newbie

Try this,

Code:

#!/usr/bin/perl
open(FH,"<","file1");
open(FH1,"<","file2");
while (<FH>) {
if(/(.+?)\s+(PPP|KKK).*/) {$hs{$1}=$2;}
}
while(<FH1>) {
if ($p) {print $_;$p=0;}
if(/\>(.+?)\s+/) {if ($hs{$1}) {print "\>",$1,"\n";$p=1;}}
}

Hey thank you so much. But however I want to create two resulting files. like a file which will be like file 1 but only contain
GKHGGSS0098 PPP.100.F.LE
GKHYXDF9081 KKK.100.F.LE

And another file like file 2 that will contain the corresponding data as printed on the screen now..

Please do let me know if I am clear