o Rŀg@sldZddlmZddlmZddlmZgdZeZGdddZdd Ze d kr4dd l m Z e d Sd S) zCode to work with the KEGG Gene database. Functions: - parse - Returns an iterator giving Record objects. Classes: - Record - A representation of a KEGG Gene. ) _default_wrap) _wrap_kegg) _write_kegg)r) $r)-rrrc@s@eZdZdZddZddZddZdd Zd d Zd d Z dS)RecordaHolds info from a KEGG Gene record. Attributes: - entry The entry identifier. - name A list of the gene names. - definition The definition for the gene. - orthology A list of 2-tuples: (orthology id, role) - organism A tuple: (organism id, organism) - position The position for the gene - motif A list of 2-tuples: (database, list of link ids) - dblinks A list of 2-tuples: (database, list of link ids) cCs4d|_g|_d|_g|_d|_d|_g|_g|_dS)zInitialize new record.rN)entryname definition orthologyorganismpositionmotifdblinksselfrJ/var/www/html/myenv/lib/python3.10/site-packages/Bio/KEGG/Gene/__init__.py__init__*s zRecord.__init__cCs|||dS)z.Return a string representation of this Record.///)_entry_name_dblinksrrrr__str__5szRecord.__str__cCtd|jgS)NENTRY)rr rrrrr9z Record._entrycCstddd|jDS)NNAMEcSsg|]}t|tdqS) wrap_rule)r name_wrap.0linerrr >sz Record._name..)rr rrrrr<sz Record._namecCr)N DEFINITION)rr rrrr _definitionArzRecord._definitioncCsDg}|jD]}||ddd|dqtddd|DS)Nr: rrDBLINKScSsg|] }t|tddqS) r!)rid_wrapr$rrrr'Isz#Record._dblinks..)rappendjoinr)rsr rrrrDs  "zRecord._dblinksN) __name__ __module__ __qualname____doc__rrrrr)rrrrrr s  r c cst}|D]}|dddkr|Vt}q|dddkr%|dd}|dd}|dkr;|}|d|_q|dkrK|d }|j|q|d krS||_q|d kri|d \}}||f}|j|q|d kr||d \}}||f} | |_q|dkr||_ q|dkr|d\} } | } | | f} |j | q|dkrd|vr|d\} } | } | | f} |j | q|j d} | \} } | || | f} | |j d<qdS)aParse 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 Nr z z ENTRY rz NAME ;z DEFINITION z ORTHOLOGY z z ORGANISM z POSITION z MOTIF r*z DBLINKS :) r stripsplitr r r.r rrrrrextend) handlerecordr&keyworddatawordsidr rrkeyvaluesrowrrrparseMs\     rF__main__) run_doctestN) r4Bio.KEGGrrrr#r-r rFr1 Bio._utilsrHrrrrs  2>