def save_orth(prots=None,ncpu=1,out_file=None,inp_orth=None): if inp_orth != None: print 'using following file as orthologs', inp_orth inp_orth=pick.load(open(inp_orth)) return inp_orth pg=PanGenomer(prots,ncpu) print 'now finding orthologs... it may take some time..' pg.run() orthologs=pg.orthologs if out_file != None: dumper=open(out_file,'w') pick.dump(orthologs, dumper) return orthologs
#
#Parse di BLASTall e costruzione grafo
#parsed=parse_blast(out)
parsed=parse_blast_bord(out,hit_thr,bord_thr,id_perc_thr)
adj_list=build_adj_list(parsed,draft,bord_thr)
network=build_network(adj_list)
#
#Scrivi file gexf e appendi alla lista dei network
graph_name=output_folder+draft.graph_name
nx.write_gexf(network,graph_name)
networks[draft.name]=graph_name
#predizione proteine e BBH seriale
prots=synteny.predictor(fastas)
pg=PanGenomer(prots,opts.ncpu)
print 'now finding orthologs... it may take some time..'
pg.run()
orthologs=pg.orthologs
relations={}
#organizzazione delle relazioni: contigui di uno stesso genoma che condividono ortologhi con contigui di altri genomi sono raggruppati
for k in orthologs:
for v1 in orthologs[k]:
for v2 in orthologs[k]:
if v1==v2:continue
draft1,contig1=from_gene_to_contig(v1)
draft2,contig2=from_gene_to_contig(v2)
relations[draft1],relations[draft2]=relations.get(draft1,{}),relations.get(draft2,{})
relations[draft1][contig2]=relations[draft1].get(contig2,[])
relations[draft2][contig1]=relations[draft2].get(contig1,[])
if contig1 not in relations[draft1][contig2]:
relations[draft1][contig2].append(contig1)
if contig2 not in relations[draft2][contig1]: