def getConservedELMs(virus, subtypes):
ls = [utils_motif.annotation2protein(os.path.join(local_settings.RESULTSDIR,
virus + '.' + subtype
+ '.elms.70.controled'),
{'ELM':True})
for subtype in subtypes[virus]]
return utils_graph.intersectLists(ls)
def expandProteinsForELMs(humanAnnotationFile, elm_pairs_dir,
useELMs, proteins, domain_tools):
prosite2protein = utils_motif.annotation2protein(humanAnnotationFile,
domain_tools)
for domain in domain_tools.keys():
f = open(elm_pairs_dir + 'ELM.' + domain + '.pairs')
for line in f.readlines():
sp = map(string.strip, line.split('\t'))
if len(sp) > 1:
if sp[1] != '':
elm = sp[0]
if useELMs.has_key(elm):
for protein in prosite2protein[ sp[1] ]:
useELMs[elm][protein] = True
if not proteins.has_key(protein): proteins[protein] = {}
proteins[protein][elm] = True
f.close()
import sys, utils_motif, utils
from collections import defaultdict
elm2proteins = utils_motif.annotation2protein(sys.argv[1], {'ELM':True})
for elm in elm2proteins:
seqs = defaultdict(utils.init_zero)
total = 0
for protein in elm2proteins[elm]:
for [st, stp, seq] in elm2proteins[elm][protein]:
seqs[seq] += 1
total += 1
for seq in seqs:
print elm + '\t' + seq + '\t' + str(seqs[seq]) + '\t' + str(float(seqs[seq])/float(total))
"../../Data/ELM/HIV-1/Subtypes_B_C/HIV1.BC.70.conserved",
"ELM",
"../../Data/ELM/Human/human.website.elm",
"ELM",
"../../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 = {}
