
# Location where raw transcriptome references downloaded from Pseudomonas.com and NCBI are stored
REF_DIR = LOCAL_DIR / "Documents" / "Data" / "Core_accessory"
PAO1_REF = REF_DIR / "Pseudomonas_aeruginosa_PAO1_107.fasta"
PA14_REF = REF_DIR / "Pseudomonas_aeruginosa_UCBPP-PA14_109.fasta"
PHAGE_REF = REF_DIR / "phage_sequences.fasta"
PILA_QUERY = REF_DIR / "pilA_pa14.fasta"

# Location of BLAST DB
BLAST_DIR = REF_DIR / "blast" / "db"
PAO1_DB_DIR = BLAST_DIR / "PAO1_DB"
PA14_DB_DIR = BLAST_DIR / "PA14_DB"
PAO1_PHAGE_DB_DIR = BLAST_DIR / "PAO1_PHAGE_DB"
PA14_PHAGE_DB_DIR = BLAST_DIR / "PA14_PHAGE_DB"
PAO1_BLAST_RESULT = BLAST_DIR / "pao1_blast_output.tsv"