Cheers for the help guys, but im still not getting it. Truth be told, i hadn't tried the script with the examples I gave you, just gave those for ease of explaination. But when a few of you said that it worked for you, I copied back what inputs I'd wrote, tried it and I get no output at all. My actual file1 and file2 are 8000 queries and 12000 lines to select from
so:
my script + my (8000) inputs = print everything
my script + made up (5) inputs = print nothing
kennethk's script + my (8000) inputs = print everything
kennethk's script + made up (5) inputs = print nothing

seen as two computers are getting two diff results is there an overall problem? I know a bad workman blames his tools but could it be?....
whats the chance of me missing some module/update/package? (clutching at straws here)

my actual files go to the tune of: 

File1
GP_MASA_01F04_c 
GP_MASA_38C02_c 
GP_MASA_33B06_c 
GP_MASA_24D04_c 
GP_MASA_35A04_c    ...to 9000 lines

File2  (is a .csv file)
'GP_MASA_01F04_c',681,'ACCACACATCATCTGACTTACGTACGTACG......
'GP_MASA_38C02_c',273,'ACATCCTTCACAGAAGTTTGT.............
'GP_MASA_33B06_c',288,'ACATACTAACACGGTCTTT...............
                      .....to 12400 lines

[download]

also, I intend to have a go with all the other scripts and tips you kind kind people have put up here but its the middle of the night and Im falling asleep where im sitting!

thank you again for all the help

In reply to Re: list lines not found in config (while+if) by tangledupinperl
in thread list lines not found in config (while+if) by tangledupinperl

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