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# GraffiTE libraries from DFAM 3.9 #
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# Last update date is given with file name
# DFAM entries are extracted for each target organism including "ancestor" and "descendant" models, i.e. repeats attributed to ancestral and lineage-specific nodes in the phylogeny. See: https://www.dfam.org/help/family
# Generic command:
# famdb.py <dfam_dir> --curated -f fasta_name -ad <taxID/'species name'> --include-class-in-name > custom_lib.fa
# with <dfam_dir> the directory where DFAM partition are downloaded (see: https://www.dfam.org/releases/current/families/FamDB/README.txt)
# famdb.py see: https://github.com/Dfam-consortium/FamDB

# Homo sapiens
./famdb.py families -ad "Homo sapiens" --curated --format fasta_name --include-class-in-name > Homo_sapiens_DFAM3.9_040926.fa
# Drosophila melanogaster
./famdb.py families -ad "Drosophila melanogaster" --curated --format fasta_name --include-class-in-name > Drosophila_melanogaster_DFAM3.9_040926.fa
# Danio rerio
./famdb.py families -ad "Danio rerio" --curated --format fasta_name --include-class-in-name > Danio_rerio_DFAM3.9_040926.fa
# Caenorhabditis elegans
./famdb.py families -ad "Caenorhabditis elegans" --curated --format fasta_name --include-class-in-name > Caenorhabditis_elegans_DFAM3.9_040926.fa
# Mus musculus
./famdb.py families -ad "Mus musculus" --curated --format fasta_name --include-class-in-name > Mus_musculus_DFAM3.9_040926.fa