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#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re
class TestFailedError(Exception):
pass
if __name__ == "__main__":
if len(sys.argv) != 2:
sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
sys.stderr.write('Test the FeatureIndex and FeatureStream bindings on GFF3_file.')
sys.exit(1)
genome_stream = GFF3InStream((sys.argv)[1])
# try to instantiate an interface -> should fail
try:
feature_index = FeatureIndex()
except NotImplementedError:
pass
else:
raise
# instantiate index object
feature_index = FeatureIndexMemory()
genome_stream = FeatureStream(genome_stream, feature_index)
feature = genome_stream.next_tree()
while feature:
feature = genome_stream.next_tree()
seqid = feature_index.get_first_seqid()
features = feature_index.get_features_for_seqid(seqid)
if not features:
raise TestFailedError
rng = feature_index.get_range_for_seqid(seqid)
features_r = feature_index.get_features_for_range(rng.start, rng.end,
seqid)
if not len(features) == len(features_r):
raise TestFailedError
gff3_visitor = GFF3Visitor()
for feature in features:
feature.accept(gff3_visitor)
if not isinstance(feature, FeatureNode):
raise TestFailedError
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