Package Bio :: Package EUtils :: Module Mixins
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Source Code for Module Bio.EUtils.Mixins

 1  """implements functionality shared between HistoryClient and DBIdsClient""" 
 2  # These are mixins and use methods implemented by the main classes. 
 3   
 4  import parse 
 5   
6 -class LinkMixin:
19 32
33 - def lcheck(self, 34 db = "pubmed", 35 term = None, 36 field = None, 37 daterange = None):
38 infile = self.elink(db = db, 39 cmd = "lcheck", 40 term = term, 41 field = field, 42 daterange = daterange) 43 return parse.parse_lcheck(infile)
44
45 - def ncheck(self, 46 db = "pubmed", 47 term = None, 48 field = None, 49 daterange = None):
50 infile = self.elink(db = db, 51 cmd = "ncheck", 52 term = term, 53 field = field, 54 daterange = daterange) 55 return parse.parse_ncheck(infile)
56
68
69 -class SequenceFetchMixin(LinkMixin):
70 pass
71 72 73 ## Should turn this into a Bio.SeqRecord object 74 ## Could do that using the XML code, but GenBank/GenPept is better. 75 ## def fetch(self, 76 ## seq_start = None, seq_stop = None, strand = None, 77 ## complexity = None): 78 ## return parse.parse_fetch_xml(self.efetch(seq_start = seq_start, 79 ## seq_stop = seq_stop, 80 ## strand = strand, 81 ## complexity = complexity)) 82
83 -class PublicationFetchMixin(LinkMixin):
84 - def fetch(self):
85 return parse.parse_fetch_publication_xml(self.efetch("xml"))
86