def __init__(self):
databases = Databases()
self.signature_modules = databases.signature_modules
self.m2def = databases.m2def()
self.modules = databases.m()
self.ko_output = "module_completeness.tsv"
self.module_paths = "module_paths.tsv"
self.aggregate_output = "aggregate_output.tsv"
def __init__(self):
d = Databases()
self.m2def = d.m2def()
self.m2c = d.m2c()
self.c = d.c()
self.m = d.m()
self.c2m = d.c2m()
self.signature_modules = d.signature_modules
self.output_file = 'linkages.tsv'
def __init__(self):
databases = Databases()
self.signature_modules = databases.signature_modules
self.m2def = databases.m2def()
self.m = databases.m()
def __init__(self, metadata, abundances_metagenome,
abundances_transcriptome, abundances_metabolome,
fisher_results):
self.abundances_metagenome = abundances_metagenome
self.abundances_transcriptome = abundances_transcriptome
self.abundances_metabolome = abundances_metabolome
self.fisher_results = fisher_results
self.metadata_keys = list(metadata.keys())
databases = Databases()
self.reaction_to_module = databases.r2m()
self.module_to_reaction = databases.m2r()
self.module_descriptions = databases.m()
self.reaction_to_pathway = databases.r2p()
self.pathway_to_reaction = databases.p2r()
self.pathway_descriptions = databases.p()
self.compound_desc_dict = databases.compound_desc_dict()
self.compound_descriptions = databases.c()
self.reaction_descriptions = databases.r()
self.reactions_to_compounds = databases.r2c()
self.reactions_to_kos = databases.r2k()
self.matrix_header = ["compound", "reaction", 'type']
self.transcriptome_header = [
key + '_reaction_transcriptome' for key in self.metadata_keys
]
self.compound_header = [
key + '_compound' for key in self.metadata_keys
]
self.metadata_header = [
'node', 'description', 'type', 'module', 'module_descr', 'pathway',
'pathway_descr', 'node_type'
]
self.query_header = ['query', 'step']
self.step_header = ['step']
self.to_omit = set([
"C00828", # Menaquinone
"C00534", # Pyridoxamine
"C00006", # NADP+
"C00003", # NAD+
"C00002", # ATP
"C00314", # Pyridoxine
"C00864", # Pantothenate
"C00504", # Folate
"C00032", # Heme
"C05443", # Vitamin D3
"C00253", # Nicotinate
"C00250", # Pyridoxal
"C11378", # Ubiquinone-10
"C05777", # Coenzyme F430
"C00072", # Ascorbate
"C00378", # Thiamine
"C00101", # Tetrahydrofolate
"C00029", # UDP-glucose
"C00068", # Thiamin diphosphate
"C00061", # FMN
"C00063", # CTP
"C05776", # Vitamin B12
"C00113", # PQQ
"C18237", # Molybdoenzyme molybdenum cofactor
"C00051", # Glutathione
"C00010", # CoA
"C00016", # FAD
"C00018", # Pyridoxal phosphate
"C00019", # S-Adenosyl-L-methionine
"C00153", # Nicotinamide
"C04628", # Coenzyme B
"C00862", # Methanofuran
"C15672", # Heme O
"C15670", # Heme A
"C02059", # Phylloquinone
"C03576", # Coenzyme M
"C05441", # Vitamin D2
"C00272", # Tetrahydrobiopterin
"C02477", # alpha-Tocopherol
"C00473", # Retinol
"C00120", # Biotin
"C00725", # Lipoate
"C00053", # 3'-Phosphoadenylyl sulfate
"C00194", # Cobamide coenzyme
"C00255", # Riboflavin
'C00001', # H2O
'C00008', # ADP
'C00013', # Diphosphate
'C00004', # NADH
'C00005', # NADPH
'C00080', # H+
'C00009', # Orthophosphate
'C00008', # ADP
'C00004', # NADH
'C00020', # AMP
'C00007', # Oxygen
'C00015'
]) # UDP