in reply to Parsing Sequence Records
You might also consider using the three argument form of open:
open(my $in, '<', "/Users/Desktop/Pipelines/fungi.1.aa.hypothetical.fa +a"); open(my $out, '>', "Users/Desktop/Pipelines/fungi.1.aa.hypothetical50. +faa");
*My* tenacity goes to eleven...
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Seekers of Perl Wisdom