def __init__(self, instream, taxon_id=None):
gt.extended.CustomStream.__init__(self)
self.iterator = FlatFileIterator(instream)
self.outqueue = collections.deque()
self.go_coll = GOCollection(taxon_id)
self.uniprots = {}
self.typemaps = {
'gene': 'pseudogene',
'mRNA': 'pseudogenic_transcript',
'rRNA': 'pseudogenic_transcript',
'tRNA': 'pseudogenic_transcript',
'exon': 'pseudogenic_exon'
}
