nwck_save2.py

def tokens(s):
    cursor=0
    n=''
    while cursor<len(s):
        if s[cursor]=='(':
            cursor+=1
            yield 'OPEN_PAREN','('
            continue
        if s[cursor]==')':
            cursor+=1
            yield 'CLOSE_PAREN',')'
            continue
        if s[cursor]==':':
            cursor+=1
            yield 'COLON',':'
        if s[cursor]==';':
            cursor=len(s)
            break
            
        if s[cursor]==',':
            cursor+=1
            yield 'COMMA',','
            continue
        n=''        
        while cursor<len(s) and s[cursor] not in [',',';',')','(',':']:
            n+=s[cursor]
            cursor+=1        
        if len(n.strip())>0:
            yield 'LABEL',n.strip()                  
             
def build_tree2(s):
    tree,labels,weights={},{},{}
    taxa=[]
    parent,curnode=-1,0
    new_node=1
    tree[0]=-1 #introduce an artificial root note
    prior_kind=None
    for (kind,value) in tokens(s):
        if kind=='OPEN_PAREN':       
            parent=curnode
            curnode=new_node
            tree[curnode]=parent
            new_node=new_node+1
            prior_kind=kind
            continue
        if kind=='LABEL':
            if prior_kind=='CLOSE_PAREN':
                labels[value]=savenode
            elif prior_kind=='COLON':
                weights[savenode]=int(value)
            else:
                labels[value]=new_node
                tree[new_node]=curnode
                savenode=new_node # needed if this label is followed by colon
                taxa.append(value)
                new_node+=1              
            prior_kind=kind
            continue
        
        if kind=='COLON':
            if prior_kind=='COMMA' or prior_kind=='OPEN_PAREN':
               tree[new_node]=curnode
              # savenode=new_node
               new_node+=1
            prior_kind=kind
            continue
                
        if kind=='CLOSE_PAREN':
            if prior_kind=='COMMA':
                tree[new_node]=curnode
                new_node+=1
            savenode=curnode
            curnode=parent
            parent=tree[curnode]
            prior_kind=kind
            continue
        if kind=='COMMA':
            if prior_kind=='COMMA':
                tree[new_node]=curnode
                new_node+=1
            prior_kind=kind
            continue
            
    if parent!=-1:
        raise Exception('ParseError')
    else:               
        return tree,labels,weights,taxa


s="((((((Agama_ammon,Latastia_lineatus),(Boiga_atthis,Bos_leporosum)),Turdus_laticauda),(Circus_acutus,Dipus_franckii)),(((((Asthenodipsas_caudatus,Passer_novaeguineae),Testudo_quadriocellata),Oedura_kopsteini),(((Basiliscus_rosmarus,(Lepidobatrachus_viridescens,Streptopelia_breitensteini)),((Butastur_hispida,Ciconia_fiber),Lepus_multifasciata)),sibiricus_aegyptia)),Hirundo_fissipes)),((Aix_erythronotus,Uroplatus_garulla),Almo_guttifer),(((((((((((((((((((((((((Alaus_fasciata,Oceanodroma_kingii),(Marmota_vegans,Phrynosoma_amethistina)),Tupinambus_vitticeps),Corallus_baeri),Ciconia_wogura),Budytes_marcianus),Ortigometra_brachydactyla),Phrynosoma_oenanthe),((((Ambystoma_taezanowskyi,Anolis_adspersus),((Monodon_stejnegeri,(Parus_walti,Phrynops_fulva)),Pogona_alterna)),((Chrysopelea_torquatus,Ninox_monachus),Riparia_cambridgei)),Phoca_carbo)),Aythya_stagnalis),Tropidurus_not),Paramesotriton_docilis),Lycaenopsis_hypomelus),Phormictopus_leucophyllata),Petrocincla_oxycephalum),Vipera_arizonensis),((Almo_carnivorus,Nyctaalus_dulkeitiana),Chelodina_dentata)),(((((((((((((Ambystoma_czerskii,(Fulica_stagnalis,(Haplopelma_multituberculatus,Phrynohyas_himalayanus))),Xenochrophis_caninus),Ptychozoon_semipalmatus),Querquedula_graeca),Haliaetus_caniceps),Machetes_laevis),(Litoria_thibetanus,Otis_grandis)),Uroplatus_platyrhinos),Parus_pardalis),(Camptoloma_constrictor,Leuciscus_iguana)),(Lamprophis_fernandi,Sorex_onocrotalus)),((((((((Boiga_gecko,Tropidurus_guentheri),Euspiza_veredus),Net_turtor),Polypedates_krueperi),Notophthalmus_hispida),Ceratophrys_kingii),(Capella_bairdi,(Paraphysa_marmorata,Sus_taxus))),Tropidurus_geyri)),Scincus_semipalmatus)),Thymallus_tristis),(Phyllopneuste_oenanthe,Psammophis_pardus)),Desnana_parahybana),Haplopelma_quadrivirgata),Egretta_insularis),((((Bronchocela_leptochelis,((Circus_mycterizans,(Dasypeltis_orientalis,(Meles_rufina,Pandinus_troglodytes))),Thymallus_alpestris)),Prunella_celer),Ziphius_bifasciatus),(Motacilla_sujfunensis,Neolycaena_yeltoniensis))),Chrttusia_davidiana));"
x,y='Psammophis_pardus', 'Phrynohyas_himalayanus'


         
def path_to_root(x,tree,labels):
    start_node=labels[x]
    path=[start_node]
    parent=tree[start_node]
    while parent!=-1:
        path.append(parent)
        parent=tree[parent]
    return path


def tree_distance(x,y,tree,labels,weights):
    xnode=labels[x]
    ynode=labels[y]
    d=0
    while True:
        if xnode<ynode:
            d+=weights.get(ynode,1)
            ynode=tree[ynode]         
        elif ynode<xnode:
            d+=weights.get(xnode,1)
            xnode=tree[xnode]
        elif ynode==xnode:
            return d
            
        
#tree,labels=build_tree2(s)

#print path_to_root(x,tree,labels)
#print path_to_root(y,tree,labels)