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"""implements functionality shared between HistoryClient and DBIdsClient"""
# These are mixins and use methods implemented by the main classes.
import parse
class LinkMixin:
def prlinks(self,
db = "pubmed",
term = None,
field = None,
daterange = None):
"""get the prlinks as a Datatypes.LinksLinkSet"""
infile = self.elink(db = db,
cmd = "prlinks",
term = term,
field = field,
daterange = daterange)
return parse.parse_prlinks(infile)
def llinks(self,
db = "pubmed",
term = None,
field = None,
daterange = None):
"""get the llinks as a Datatypes.LinksLinkSet"""
infile = self.elink(db = db,
cmd = "llinks",
term = term,
field = field,
daterange = daterange)
return parse.parse_llinks(infile)
def lcheck(self,
db = "pubmed",
term = None,
field = None,
daterange = None):
infile = self.elink(db = db,
cmd = "lcheck",
term = term,
field = field,
daterange = daterange)
return parse.parse_lcheck(infile)
def ncheck(self,
db = "pubmed",
term = None,
field = None,
daterange = None):
infile = self.elink(db = db,
cmd = "ncheck",
term = term,
field = field,
daterange = daterange)
return parse.parse_ncheck(infile)
def neighbor_links(self,
db = "pubmed",
term = None,
field = None,
daterange = None):
infile = self.elink(db = db,
cmd = "neighbor",
term = term,
field = field,
daterange = daterange)
return parse.parse_neighbor_links(infile)
class SequenceFetchMixin(LinkMixin):
pass
## Should turn this into a Bio.SeqRecord object
## Could do that using the XML code, but GenBank/GenPept is better.
## def fetch(self,
## seq_start = None, seq_stop = None, strand = None,
## complexity = None):
## return parse.parse_fetch_xml(self.efetch(seq_start = seq_start,
## seq_stop = seq_stop,
## strand = strand,
## complexity = complexity))
class PublicationFetchMixin(LinkMixin):
def fetch(self):
return parse.parse_fetch_publication_xml(self.efetch("xml"))
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