) / len(reactions_with_gene)
ont = self.db.ontologies.find_one({"term": pw.lower()})
if ont:
name = ont["name"]
else:
name = pw
pw_obj = PathwaySumary(term=pw,
name=name,
count=pws_dict[pw]["genes"],
properties=pws_dict[pw])
self.pathways.append(pw_obj)
if __name__ == "__main__":
from SNDG.BioMongo.Process.BioMongoDB import BioMongoDB
from SNDG.BioMongo.Process.Importer import _common_annotations, _protein_iter, import_kegg_annotation, \
index_seq_collection, build_statistics, load_pathways
mdb = BioMongoDB("tdr", port=27018)
# ps = PathwaysAnnotator(mdb.db, "SaureusN315", "/data/organismos/SaureusN315/pathways/")
# ps.sbml("Red_Staphylo_Curada_rs.sbml")
# ps.species_filter("allfilters_con_c.dat")
# ps.extract_genes_from_notes(lambda notes: gene_name_regexp.findall(notes))
# ps.annotate()
# index_seq_collection(mdb.db, "SaureusN315", pathways=True, go=True, keywords=True, ec=True, organism_idx=True,
# structure=False)
build_statistics(mdb.db, "SaureusN315")
from SNDG.BioMongo.Process.Importer import load_pathways, build_statistics
from SNDG.BioMongo.Process.BioCyc2Mongo import BioCyc
from SNDG.BioMongo.Process.BioMongoDB import BioMongoDB
from SNDG.BioMongo.Model.SeqCollection import SeqCollection
import pymongo
port = 27018
mdb = BioMongoDB("tdr", port=port)
db = pymongo.MongoClient(port=port).pdb
load_pathways("cruzi",
"/data/organismos/cruzi/pathways/pathways-sm.sbml",
mdb.db,
"/data/organismos/cruzi/pathways/",
filter_file="allfilters_con_c.dat")
biocyc = BioCyc(mdb.db)
biocyc.user = BioMongoDB.demo
biocyc.pre_build_index(SeqCollection.objects(name="cruzi").get())
build_statistics(mdb.db, "cruzi")
load_pathways(name,
"/data/organismos/" + name +
"/annotation/pathways/small.sbml",
mdb.db,
"/data/organismos/" + name + "/annotation/pathways",
gregexp="\(([\-\w\.]+)\)",
filter_file="allfilters_con_c.dat")
index_seq_collection(mdb.db,
name,
pathways=True,
go=True,
keywords=True,
ec=True,
organism_idx=True,
structure=False)
build_statistics(mdb.db, name)
import subprocess as sp
for xx in orgs:
x = xx[0]
for y in tqdm(
glob("/data/organismos/" + x +
"/estructura/sndg/modelos/*.pocket.json")):
sp.call("ln %s %s" %
(y, ("/data/organismos/%s/estructura/sndg/pockets/" % x) +
y.split("/")[-1].replace(".pdb.pocket", "")),
shell=True)
# rsync -avzh /data/organismos/Mbovis/estructura/sndg/pockets/* marvin:/data/organismos/Mbovis/estructura/sndg/pockets/
# rsync -avzh /data/organismos/Mbovis/estructura/sndg/modelos/*.pdb marvin:/data/organismos/Mbovis/estructura/sndg/modelos/
# 200918,
# 200930,
# 200938,
# 200940,
# 201174,
# 203682,
# 203691,
# 204441,
# 204455,
# 204457,
# 267890,
# 508458,
# 544448,
# 578822,
# 1293497,
# 2157}
#
# from SNDG.BioMongo.Process.BioCyc2Mongo import BioCyc
# biocyc = BioCyc("saureus")
# biocyc.complete_pathways("ILEX_PARA2", "/data/databases/biocyc/metacyc/pathways.dat",
# "/data/databases/biocyc/metacyc/reactions.dat", filter_tax)
index_seq_collection(mdb.db,
"ILEX_PARA",
ec=True,
go=False,
keywords=True,
organism_idx=True,
pathways=True,
structure=False)
build_statistics(mdb.db, "ILEX_PARA")