def get_tree_info(id_map):
taxon_map = {}
gene_seq_map = {}
species_map = {}
for label, seqid in id_map.iteritems():
print >> sys.stderr, "processing ", label, seqid
idp = miscParses.parsed_accID(seqid)
# now we annotate it with (a) species name; (b) closest downstream gene description
r = NCBI.get_acc_gb(idp.acc)
species_name = r.annotations['organism']
species_map[idp.acc] = species_name
if idp.strand == +1:
gene = NCBI.get_closest_downstream_gene(r, idp.end, idp.strand)
else:
gene = NCBI.get_closest_downstream_gene(r, idp.start, idp.strand)
if gene is None:
taxon_map[label] = 'Unknown'
gene_seq_map[seqid] = None
continue
# TODO: put this into a phyloXML format!!
# for now....let's just do normal newick
gene_seq_map[seqid] = gene
newname = label + '-' + species_name + '::'
if 'product' in gene.qualifiers:
newname += gene.qualifiers['product'][0]
elif 'note' in gene.qualifiers:
newname += gene.qualifiers['note'][0]
elif 'gene' in gene.qualifiers:
newname += gene.qualifiers['gene']
taxon_map[label] = newname
return taxon_map, gene_seq_map, species_map
def map_tree_taxon(tree_filename, id_map):
taxon_map = {}
gene_seq_map = {}
t = dendropy.Tree.get_from_path(tree_filename, 'newick')
for n in t.leaf_nodes():
# n.taxon.label is like 'T1', id_map maps back to <acc>/<start>-<end>
idp = miscParses.parsed_accID(id_map[n.taxon.label])
# now we annotate it with (a) species name; (b) closest downstream gene description
r = NCBI.get_acc_gb(idp.acc)
species_name = r.annotations['organism']
if idp.strand == +1:
gene = NCBI.get_closest_downstream_gene(r, idp.end, idp.strand)
else:
gene = NCBI.get_closest_downstream_gene(r, idp.start, idp.strand)
# TODO: put this into a phyloXML format!!
# for now....let's just do normal newick
gene_seq_map[n.taxon.label] = gene.qualifiers['translation']
newname = n.taxon.label + '-' + species_name + '::' + gene.qualifiers['product'][0]
taxon_map[n.taxon.label] = newname
n.taxon.label = newname
return t, taxon_map, gene_seq_map
print('6:Récupérer et afficher une entrée Prosite ')
print(
"7:Lancer un scan avec l'outil ScanProsite et afficher les motifs trouvés"
)
print('8:Traduire une signature Prosite en une expréssion Python')
print('9:Vérifier si une signature existe dans une séquence')
print(
'10:Télécharger une entrée PDB puis afficher cette entrée ou non selon votre choix '
)
print("Q: Pour Quitter")
choix = input("Entrez votre choix: ")
if choix == '1':
Lecture.Programme()
elif choix == '2':
NCBI.programme()
elif choix == '3':
Recuperer_SwissProt.programme()
elif choix == '4':
AlignementGlobLoc.programme()
elif choix == '5':
Fragmentation.programme()
elif choix == '6':
RecupererEntreeProsite.programme()
elif choix == '7':
ScanProsite.programme()
