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$ 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
...
          'Q6GZX4' => 'PF04947.9',
          'Q39371' => 'PF01486.12 PF00319.13'
        };