Do your files have empty lines which don't match your regexps? Try returning empty list (
()) in case the regexp didn't match (
map will omit the element in this case):
$ perl -w -MData::Dumper -E'%h = map {if(/(.+)\s+\|\s+(.+)/){$1=>$2}el
+se{()}} (<>); print Dumper \%h'
Q6GZX4 | PF04947.9
Q96355 | PF01486.12 PF00319.13
Q96356 | PF01486.12 PF00319.13
Q39371 | PF01486.12 PF00319.13
DSFSDF ASD SSSSSSSSSS
^D
$VAR1 = {
'Q96355' => 'PF01486.12 PF00319.13',
'Q96356' => 'PF01486.12 PF00319.13',
'Q6GZX4' => 'PF04947.9',
'Q39371' => 'PF01486.12 PF00319.13'
};
Edit: return an empty list
Sorry if my advice was wrong.