preprocess/constants.py at main · MetaGSC/preprocess · GitHub

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thread_count = 8
frag_len = 5000
coverage = 2
k = 7
err_file = "error.txt"
log_file = "log.txt"

# databases
# plas_db_path = "../databases/DNA-ML_FYP_2021/plasmid_refs"
# chrom_db_path = '../databases/DNA-ML_FYP_2021/bacterial_references'
plas_db_path = "../../databases/DNA-ML_FYP_2021/plas-ref-tiny"
chrom_db_path = '../../databases/DNA-ML_FYP_2021/bact-ref-tiny'
db_path = "../../references/biomarkerdbs"

# fragment files
plas_write_path = "results/plasmid/fragments"
chrom_write_path = "results/chromosome/fragments"
extra_plasmid_write_path = "results/extra-plasmid/fragments"

# fragment txt files
plas_txt_write_path = "results/plasmid/extra/frag-txt"
chrom_txt_write_path = "results/chromosome/extra/frag-txt"
extra_plasmid_txt_write_path = "results/extra-plasmid/extra/frag-txt"

# kmer files
plas_7mer_out_path = "results/plasmid/extra/7mer-out"
chrom_7mer_out_path = "results/chromosome/extra/7mer-out"
ex_plas_7mer_out_path = "results/extra-plasmid/extra/7mer-out"

plas_7mer_write_path = "results/plasmid/7mers"
chrom_7mer_write_path = "results/chromosome/7mers"
ex_plas_7mer_write_path = "results/extra-plasmid/7mers"

# circularity files
plas_circ_write_path = "results/plasmid/circular"
chrom_circ_write_path = "results/chromosome/circular"
ex_plas_circ_write_path = "results/extra-plasmid/circular"

plas_circ_out_path = "results/plasmid/extra/nucmer_out"
chrom_circ_out_path = "results/chromosome/extra/nucmer_out"
ex_plas_circ_out_path = "results/extra-plasmid/extra/nucmer_out"

plas_frag_split_path = "results/plasmid/extra/split"
chrom_frag_split_path = "results/chromosome/extra/split"
ex_plas_frag_split_path = "results/extra-plasmid/extra/split"

# inc factor files
plas_inc_out_path = "results/plasmid/extra/blastn-out"
chrom_inc_out_path = "results/chromosome/extra/blastn-out"
ex_plas_inc_out_path = "results/extra-plasmid/extra/blastn-out"

plas_inc_write_path = "results/plasmid/inc-fac"
chrom_inc_write_path = "results/chromosome/inc-fac"
ex_plas_inc_write_path = "results/extra-plasmid/inc-fac"

# rrna files
plas_rrna_write_path = "results/plasmid/rrna"
chrom_rrna_write_path = "results/chromosome/rrna"
ex_plas_rrna_write_path = "results/extra-plasmid/rrna"

plas_rrna_out_path = "results/plasmid/extra/rrna-out"
chrom_rrna_out_path = "results/chromosome/extra/rrna-out"
ex_plas_rrna_out_path = "results/extra-plasmid/extra/rrna-out"

# orit files
plas_orit_out_path = "results/plasmid/extra/orit-out"
chrom_orit_out_path = "results/chromosome/extra/orit-out"
ex_plas_orit_out_path = "results/extra-plasmid/extra/orit-out"

plas_orit_write_path = "results/plasmid/orit"
chrom_orit_write_path = "results/chromosome/orit"
ex_plas_orit_write_path = "results/extra-plasmid/orit"

# mobilization, conjugation, replication files
plas_mob_out_path = "results/plasmid/extra/mob-out"
chrom_mob_out_path = "results/chromosome/extra/mob-out"
ex_plas_mob_out_path = "results/extra-plasmid/extra/mob-out"

plas_rep_out_path = "results/plasmid/extra/rep-out"
chrom_rep_out_path = "results/chromosome/extra/rep-out"
ex_plas_rep_out_path = "results/extra-plasmid/extra/rep-out"

plas_con_out_path = "results/plasmid/extra/con-out"
chrom_con_out_path = "results/chromosome/extra/con-out"
ex_plas_con_out_path = "results/extra-plasmid/extra/con-out"

plas_mob_write_path = "results/plasmid/mobilization"
chrom_mob_write_path = "results/chromosome/mobilization"
ex_plas_mob_write_path = "results/extra-plasmid/mobilization"

plas_rep_write_path = "results/plasmid/replication"
chrom_rep_write_path = "results/chromosome/replication"
ex_plas_rep_write_path = "results/extra-plasmid/replication"

plas_con_write_path = "results/plasmid/conjugation"
chrom_con_write_path = "results/chromosome/conjugation"
ex_plas_con_write_path = "results/extra-plasmid/conjugation"