SYNOPSIS

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


    search-key [search-key ...] | --name-list file.txt | --id-list file.txt

DESCRIPTION

blt extract-seq searches a GFF3 file for a feature of feature-type (e.g. gene, CDS, exon) and a substring of the attributes field. If found, extracts the sequence for that feature and all subfeatures from the corresponding FASTA file and prints the sequences to the standard output in FASTA format using part of the GFF data as the description line.

Search-key is any exact substring of the attributes column in the GFF, without regard for upper/lower case. To match a gene name exactly, include ';' in the search key. e.g. View your GFF file with "more file.gff3" to get ideas for search-key.

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 and release.

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