Closed Tong-Chen closed 2 months ago
Is your feature request related to a problem? Please describe. No
Describe the solution you'd like In agat, Bio::DB::Fasta->new is used to index FASTA files, could this module support gzipped fasta.
Bio::DB::Fasta->new
I have tried:
agat_sp_extract_sequences.pl
open(my $FASTA_INPUT_FH, "zcat $opt_fastafile |") or die "gunzip $opt_fastafile: $!"; my $db = Bio::DB::Fasta->new($FASTA_INPUT_FH);
agat_sp_extract_sequences.pl -g <(gunzip infile.gff.gz) -f <(guznip infile.fasta.gz)
This may be the question of BioPerl.
Thank!
Tong Chen
To my knowledge Bio::DB::Fasta does not allow to read compressed file. You should contact bioperl developer to get better information https://github.com/bioperl/bioperl-live
Is your feature request related to a problem? Please describe. No
Describe the solution you'd like In agat,
Bio::DB::Fasta->new
is used to index FASTA files, could this module support gzipped fasta.I have tried:
agat_sp_extract_sequences.pl
by supplying a file handle toBio::DB::Fasta->new
, which does not work.agat_sp_extract_sequences.pl -g <(gunzip infile.gff.gz) -f <(guznip infile.fasta.gz)
to deal with gzipped files. This also does not work.This may be the question of BioPerl.
Thank!
Tong Chen