def predict_die(useELMs, domain_tools, netFile):
h1 = {}
h2 = {}
net = utils_graph.getEdges(netFile)
proteins = {}
tool_d = {}
tool_d['ELM'] = True
protein2elm = utils_motif.protein2annotation('/home/perry/Projects/Human_Virus/Data/human.annotations', tool_d)
getProteinsForELMs(useELMs, proteins)
expandProteinsForELMs(useELMs, proteins, domain_tools)
for g1 in proteins.keys():
if net.has_key(g1):
for elm in proteins[g1].keys():
for g2 in protein2elm.keys():
if net[g1].has_key(g2) and protein2elm[g2].has_key(elm) and g1 != g2:
if not h1.has_key(elm): h1[elm] = {}
if not h2.has_key(elm): h2[elm] = {}
h1[elm][g1] = True
h2[elm][g2] = True
return [h1, h2]
"../../Data/ProfileScan/all.ProfileScan.scanHPRD.notNCBI",
"ProfileScan",
"../../Data/Network/Human/HPRD/hprd.intr",
"../../Data/human.hprd.prosite",
"../../Data/Network/Human/HPRD/version2entrezgeneid",
"../../Data/Binding_Relations/ELM.ProfileScan.pairs",
"some out 1",
"some out 2",
]
utils_scripting.checkStart(sys.argv, req_args, examples, len(req_args), True)
virus_elm2protein = utils_motif.annotation2protein(sys.argv[1], {sys.argv[2]: True})
study_hps = utils_graph.getNodes(sys.argv[8])
human_elm2protein = utils_motif.annotation2protein_forProteins(sys.argv[3], {sys.argv[4]: True}, study_hps)
human_cd2protein = utils_motif.annotation2protein_forProteins(sys.argv[5], {sys.argv[6]: True}, study_hps)
network = utils_graph.getEdges(sys.argv[7])
version2geneid = utils_humanVirus.get_version2entrez(sys.argv[9])
elm2cd = utils_humanVirus.get_elm2prosites(sys.argv[10])
outf1 = sys.argv[11]
outf2 = sys.argv[12]
vp_to_h1_to_h2 = {}
with open(outf1, "w") as f:
for elm in virus_elm2protein.keys():
if human_elm2protein.has_key(elm):
h2_noRestrictions = human_elm2protein[elm]
h2 = {}
h1 = {}
h1_to_h2 = {}
elms_in_module = elm.split(":")
matching_cds = {}
import utils_graph
edges = utils_graph.getEdges("/home/perry/bioperry/Projects/Thesis/Data/Network/Human/HPRD/hprd.intr")
p = utils_graph.getTopXconnectedProteins(edges, 10)
