Could Bio::DB::Fasta support gzipped FASTA?

[Tong-Chen]

Could Bio::DB::Fasta support gzipped FASTA or file handler?

open(my $FASTA_INPUT_FH, "zcat $opt_fastafile |") or die "gunzip $opt_fastafile: $!";   
my $db = Bio::DB::Fasta->new($FASTA_INPUT_FH);

Best,

Tong Chen

[cjfields]

To follow up on this: at the moment this project is completely community-driven but I'd categorize it as in maintenance mode. We will gladly add support if a volunteer wants to fork the repository and make a pull request: make appropriate updates, provide example test data, and update tests.

I'd say that such support would be great in theory but it wouldn't really be possible with standard gzip FASTA. To really support this well would likely require a bgzip based index (e.g. meaning the files should be compressed with bgzip vs gzip).