I think Bio::SeqIO from bioperl is probably still the recommended solution rather than rolling your own parser. That aside you’re missing parens on open when you create your output file so it’s not parsing the way you intend and you may not be seeing errors from there if you do have problems. Using the three arg open and parens would be better/current best practice. 

my $outfile = qq{$path/$name.faa};
open( my $out_fh, q{>}, $outfile ) or die qq{problem writing to ‘$outf
+ile’: $!};

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The cake is a lie.
The cake is a lie.
The cake is a lie.

In reply to Re: Extract multiple lists od Identifiers from a FASTA file by Fletch
in thread Extract multiple lists od Identifiers from a FASTA file by joluito

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