def __str__(self): """For backwards compatibility. TODO should eventually be replaced by AmosGenericMessage.__str__()""" buffer = [ '{RED' ] buffer.append( 'iid:%d' % self.iid ) if (self.eid != ''): # tigger doesn't like a null eid field buffer.append( 'eid:%s' % self.eid ) buffer.append( 'seq:\n%s\n.' % prettyprint( self.seq ) ) buffer.append( 'qlt:\n%s\n.' % prettyprint( self.qlt ) ) buffer.append( 'frg:%d' % self.frg ) buffer.append( 'clr:%s' % self.clr ) buffer.append( '}' ) return '\n'.join(buffer)
def toFasta(self): lineLength = 60 id = self.eid if id == '': id = self.iid buffer = ">%s\n" % id buffer += prettyprint(self.seq, lineLength) return buffer