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)