import os
from .config import Config
from .helpers import (
MappingPaths,
PathwayComplementarity,
Faprotax,
NetworkHandler,
AbdTableHandler,
SeedComplementarityHandler,
BinsHandler,
manta_input_net,
otf_seqid_ncbi_gtdb_map
)
from .utils import (
mtg_logger,
ko_list_parser,
merge_ko,
extend_complements,
load_phenotypic_traits,
extend_faprotax,
)
from .pathway_complementarity import (
export_pathway_complementarities,
all_complements,
all_alternatives,
build_kegg_url,
)
from .seed_complementarity import (
ExportSeedComplementarities,
load_seed_complement_files,
build_url_with_seed_complements,
kegg_module_related_intersect,
)
try:
from .db import (
GetPhenotrexTraits,
get_genomes_for_ncbi_tax_id,
get_ncbi_tax_id_for_genome,
patric_from_gc_list,
get_path_compls_for_ncbi_ids
)
except Exception:
print(
"mysql-connector-python is not installed in the running environment."
"Dependency and microbetag features required only for on-the-fly version."
)
pass
from .genres import (
GEMSReconstruction
)
from .networks import (
get_edgelist,
build_base_graph,
read_cyjson
)
from .tools import (
run_faprotax,
run_flashweave,
run_manta,
phenotrex_predict,
phenotrex_genotype,
kegg_annotation,
run_prodigal,
hmmsearch,
run_seed_complementarity,
)
from .build_mtg_cx2 import mtg_annotate_network
from .microbetag import (
run_microbetag
)
_KEGG_MAPPINGS = os.path.join(os.path.dirname(__file__), "mtg_maps_models", "kegg_mappings")
_KEGG_TERMS_PER_MODULE = os.path.join(_KEGG_MAPPINGS, "kegg_terms_per_module.tsv")
_MODULE_DEFINITION_MAP = os.path.join(_KEGG_MAPPINGS, "module_definition_map.json")
_KEGG_MODULES_TO_MAPS = os.path.join(_KEGG_MAPPINGS, "module_map_pairs.tsv")
_MTG_PHEN_ENV = "mtg-phenotrex"
_MTG_MODELSEED_ENV = "mtg-modelseed"
[docs]
__license__ = "GNU GPL3"
[docs]
__authors__ = ["Haris Zafeiropoulos <haris.zafeiropoulos@kuleuven.be>"]
[docs]
__cite__ = (
"Zafeiropoulos H, Michail Delopoulos EI, Erega A, Schneider A, Geirnaert A, Morris J, Faust K."
"microbetag: simplifying microbial network interpretation through annotation, enrichment tests and metabolic complementarity analysis."
"bioRxiv. 2024:2024-10."
)