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orgs.py
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orgs.py
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"""This file contains lists of organisms"""
test_orgs = ["Escherichia_coli",
"Pseudomonas_aeruginosa",
"Haemophilus_influenzae"]
orgs = ["Acinetobacter_ADP1",
"Pseudomonas_fluorescens",
"Acinetobacter_baumannii",
"Pseudomonas_fulva",
"Azotobacter_vinelandii",
"Pseudomonas_mendocina",
"Cellvibrio__gilvus",
"Pseudomonas_putida",
"Cellvibrio_japonicus",
"Pseudomonas_stutzeri",
"Pseudomonas_syringae",
"Moraxella_catarrhalis",
"Psychrobacter_arcticus_273",
"Pseudomonas_aeruginosa",
"Psychrobacter_cryohalolentis",
"Pseudomonas_brassicacearum",
"Psychrobacter_PRwf",
"Pseudomonas_entomophila"]
gammas = ["Haemophilus_influenzae",
"Escherichia_coli",
"Salmonella_typhimurium",
"Shewanella_oneidensis",
"Vibrio_cholerae"
]
firmicutes = ["Bacillus_subtilis",
"Lactobacillus_plantarum",
"Lactococcus_lactis",
"Bacillus_halodurans",
"Enterococcus_faecalis",
]
#
actinos = ["Arthrobacter",
"Mycobacterium_smegmatis",
"Streptomyces_coelicolor",
"Bifidobacterium_breve",
"Corynebacterium_diphtheriae"]
misc = ["Helicobacter_pylori_HPAG1",
]
enteros = ["Enterococcus_faecalis",
"Bifidobacterium_breve",
"Bacteroides_thetaiotaomicron",
"Fusobacterium_nucleatum",
"Lactobacillus_gasseri",
"Proteus_mirabilis",
"Escherichia_coli",
"Eubacterium_rectale"]
acinetos = ["Acinetobacter_baumannii",
"Acinetobacter_ADP1",
"Acinetobacter_calcoaceticus",
"Acinetobacter_oleivorans"]
pseudos = [org for org in orgs if "Pseudo" in org]
psychros = [org for org in orgs if "Psychro" in org]
all_orgs = list(set(orgs + gammas + firmicutes + actinos + enteros))
new_orgs = gammas + firmicutes
pvp_orgs = pseudos + psychros
last_orgs = pvp_orgs + new_orgs + actinos
ecoli = "Escherichia_coli"
group_names = ["pseudos","psychros","pvp_orgs","gammas",
"firmicutes","enteros","actinos","last_orgs"]
def org_group(org):
# lookup = {"pseudos":pseudos,
# "psychros":psychros,
# "gammas":gammas,
# "firmicutes":firmicutes,
# "actinos":actinos,
# "enteros":enteros,
# "all_orgs":all_orgs
# }
for group in ["pseudos",
"psychros",
"gammas",
"firmicutes",
"actinos",
"enteros",
"all_orgs"]:
if org in lookup[group]:
return group
assert False, "couldn't find %s in lookup table" % org
del(org) # namespace leak