zoospotter.py

def zoospotter(zoo,fn='pubmed_scored.csv', assoclist=['infection']):
    """
    Method that downloads the number of Pubmed entries associataed with a given species listed in the zoo variable.
    The variable assoclist has the fields sought.
    :param zoo: list of species names
    :param fn: file name to save.
    :param assoclist: list of terms that one wishes to see the association. E.g. 'infection' to find pathogenicity.
    :return: None.
    """
    #debugprint=print
    debugprint=lambda *x: None
    debugprint('MODE: Pubmed association')
    def get_count(terms):
        handle = Entrez.esearch(db="pubmed", term=' AND '.join(terms))
        record = Entrez.read(handle)
        handle.close()
        return record["Count"]
    Entrez.email = EMAIL
    w=csv.DictWriter(open(fn,'w',newline=''),fieldnames=['name']+['PM_'+s for s in ['plain']+assoclist])
    w.writeheader()
    for species in zoo:
        data={'name':species}
        bn=genomeArk.binomialiser(species)
        if bn:
            sp='{genus} {species}'.format(**bn)
            n = get_count([sp])
            print(species, '>>> ', sp, ' — ','x', ': ', n)
            data['PM_plain']=n
            for assoc in assoclist:
                n=get_count([sp, assoc])
                print(species,'>>> ',sp,' — ',assoc,': ',n)
                data['PM_'+assoc]=n
            debugprint(data)
        w.writerow(data)