Bio.KEGG.Gene package¶
Module contents¶
Code to work with the KEGG Gene database.
Functions: - parse - Returns an iterator giving Record objects.
Classes: - Record - A representation of a KEGG Gene.
-
class
Bio.KEGG.Gene.
Record
¶ Bases:
object
Holds info from a KEGG Gene record.
- Attributes:
entry The entry identifier.
name A list of the gene names.
definition The definition for the gene.
orthology A list of 2-tuples: (orthology id, role)
organism A tuple: (organism id, organism)
position The position for the gene
motif A list of 2-tuples: (database, list of link ids)
dblinks A list of 2-tuples: (database, list of link ids)
-
__init__
(self)¶ Initialize new record.
-
__str__
(self)¶ Return a string representation of this Record.
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Bio.KEGG.Gene.
parse
(handle)¶ Parse a KEGG Gene file, returning Record objects.
This is an iterator function, typically used in a for loop. For example, using one of the example KEGG files in the Biopython test suite,
>>> with open("KEGG/gene.sample") as handle: ... for record in parse(handle): ... print("%s %s" % (record.entry, record.name[0])) ... b1174 minE b1175 minD