def setUp(self):
self.fn = './res/INPUT.FASTA'
self.distance_threshold = ".015"
self.min_overlap = "500"
self.ambiguity_handling = "AVERAGE"
self.created_hivcluster = hivcluster.start(self.fn,
self.distance_threshold,
self.min_overlap, self.ambiguity_handling)
# the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
import datamonkey.hivcluster as hivcluster
import time
mail = '*****@*****.**'
fn = './res/INPUT.FASTA'
distance_threshold = ".015"
min_overlap = "500"
ambiguity_handling = "AVERAGE"
hc = hivcluster.start(fn, distance_threshold, min_overlap, ambiguity_handling, mail)
hivcluster.get(hc.id)
if hc.status == "Completed":
print hc.graph_dot
print hc.cluster_csv
else:
print hc.status
