blt(extract-seq)

SYNOPSIS

blt extract-seq file.gff3 file.fasta feature-type feature-name

DESCRIPTION
blt extract-seq searches a GFF3 file for a feature of feature-type (e.g. gene, CDS, exon) and if found, extracts the sequence for that feature from the corresponding FASTA file. It is the user's responsibility to ensure that the GFF and FASTA files are compatible. They should be from the same source (NCBI, Ensemble, etc) and the same genome build.

EXAMPLES
blt extract-seq Danio_rerio.GRCz11.104.gff3 \
    Danio_rerio.GRCz11.dna.primary_assembly.fa gene jun

SEE ALSO
blt(1)

AUTHOR
J. Bacon