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src/p/h/phyloGenerator-HEAD/phyloGenerator.py   phyloGenerator(Download)
    while finished <= maxCheck:
        try:
            handleSearch = Entrez.esearch(db="taxonomy", term=spName)
            resultsSearch = Entrez.read(handleSearch)
            handleSearch.close()
    while finished <= maxCheck:
        try:
            handleSearch = Entrez.esearch(db="taxonomy", term=searchTerm)
            resultsSearch = Entrez.read(handleSearch)
            finished = maxCheck + 1
def findLineage(spName):
    """Finds lineage (taxonomy) of a species.
    Returns [genus, family, ...]"""
    try:
        handleSpName = Entrez.esearch(db="taxonomy", term=spName)
def eSearch(term, retStart=0, retMax=20, usehistory="y"):
    finished = 0
    while finished <= maxCheck:
        try:
            handle = Entrez.esearch(db="nucleotide",term=term, usehistory=usehistory, retStart=retStart, retMax=retMax, retmode="text")

src/i/v/ivy-phylo-20120228/ivy/genbank.py   ivy-phylo(Download)
def gi2webenv(gilist):
    h = Entrez.esearch(
        db="nucleotide", term=" OR ".join(gilist), usehistory="y",
        retmax=len(gilist)
        )
def ac2gi(ac):
    global email
    assert email, "set email!"
    Entrez.email = email
    h = Entrez.esearch(db="nucleotide", term=ac, retmax=1)
        v = list(v)
        h = Entrez.esearch(
            db="nucleotide",
            term=" OR ".join([ "%s[ACCN]" % x for x in v ]),
            usehistory="y"
def search_taxonomy(q):
    global email
    assert email, "set email!"
    Entrez.email = email
    h = Entrez.esearch(db="taxonomy", term=q)

src/p/u/pubmedpy-HEAD/author_networks/author_net_functions.py   pubmedpy(Download)
def download_from_pubmed(search_term, filename, ret_number):
    """Downloads up to 2000 abstracts as an xml and saves it"""
    handle = Entrez.esearch(db="pubmed", term=search_term, retmode="xml", 
        RetMax=ret_number)
 
def article_search(db, search_str):
    handle = Entrez.esearch(db=db,term=search_str)
    record = Entrez.read(handle)
    article_ids = record["IdList"]
    print "Found %s articles" % len(article_ids)

src/p/u/pubmedpy-HEAD/isi/my_functions.py   pubmedpy(Download)
def get_pmid(search_term, ret_number):
    """Downloads up to 2000 abstracts as an xml and saves it"""
    handle = Entrez.esearch(db="pubmed", term=search_term, retmode="xml", 
        RetMax=ret_number)
 

src/c/l/clusterDbAnalysis-HEAD/scripts/downloadGenbankFromNCBI.py   clusterDbAnalysis(Download)
    # The default limit of 20 entries returned is not sufficient for incomplete genomes
    # which can have > 100 contigs. I think 1000 is a reasonable limit...
    genomeIDs = Entrez.read(Entrez.esearch(db="nucleotide", term = term, retmax=1000))
    nucIDs = nucIDs + genomeIDs['IdList']
    #make unique (should be already)
def accessionID_to_genbankIDs(accession):
    '''Search NCBI for the ID (the unique numerical key) for a specific genbank file from an accession ID'''
    genbank = Entrez.read(Entrez.esearch(db="nucleotide", term=accession))
    IDlist = genbank['IdList']
    #TODO: find the most recent version?
        sys.stderr.write("Querying NCBI with query: %s\n" %(query))
        # The default retmax is 20 which is way too few for some queries...
        NCBIdata = Entrez.read(Entrez.esearch(db="taxonomy", term=query, retmax=10000))
        #there can me multiple records returned
        taxon_strainIDs = NCBIdata['IdList']

src/b/i/biopython-HEAD/Scripts/query_pubmed.py   biopython(Download)
 
    if count_only:
        handle = Entrez.esearch(db="pubmed", term=query)
    else:
        handle = Entrez.esearch(db="pubmed", term=query, usehistory="Y")

src/b/i/biopython-1.63/Scripts/query_pubmed.py   biopython(Download)
 
    if count_only:
        handle = Entrez.esearch(db="pubmed", term=query)
    else:
        handle = Entrez.esearch(db="pubmed", term=query, usehistory="Y")

src/p/y/PyCon2013_SNA-HEAD/src/pubmed/pubmed.py   PyCon2013_SNA(Download)
def get_article_ids(term):
    num_records=get_number_of_records(term)
    handle = Entrez.esearch(db="pubmed", term=term, retmax=num_records)
    record = Entrez.read(handle)
    idlist = record["IdList"]

src/p/y/pymol-psico-HEAD/psico/snp.py   pymol-psico(Download)
 
    # get first protein that matches query
    handle = Entrez.esearch(db="protein", term='(%s) AND srcdb_refseq[PROP]' % (query), retmax=1)
    record = Entrez.read(handle)
    if int(record['Count']) == 0:
 
    # get snp-list for protein
    handle = Entrez.esearch(db="snp", term="%s[accn]" % (accn), retmax=100)
    record = Entrez.read(handle)
    print 'Number of SNP records: ' + record['Count']

src/j/c/jcvi-HEAD/apps/entrez.py   jcvi(Download)
    """
    for name in list_of_names:
        handle = Entrez.esearch(db='Taxonomy', term=name, retmode="xml")
        records = Entrez.read(handle)
        yield records["IdList"][0]
        while not success:
            try:
                search_handle = Entrez.esearch(db=db, retmax=retmax, term=term)
                rec = Entrez.read(search_handle)
                success = True

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