Example #1
0
 def setUp(self):
     self.mail = '*****@*****.**'
     self.fn   = './res/HIV_gp120.nex'
     self.datatype = 0
     self.gencodeid = 0
     self.created_msa = msa.upload_file(self.fn, self.datatype,
                                        self.gencodeid, self.mail)
Example #2
0
    def setUp(self):
        self.mail = '*****@*****.**'
        self.fn   = './res/HIV_gp120.nex'
        self.datatype = 0
        self.gencodeid = 0
        self.type = 'bsrel'
        self.created_analysis = msa.upload_file(self.fn, self.datatype,
                                           self.gencodeid, self.mail)

        self.bsrel_params = {
            'treemode'    : 0,
        }

        self.bsrel_analysis = analysis.create_analysis(self.created_analysis.id,
                                                      self.type,
                                                      self.bsrel_params)
Example #3
0
    def setUp(self):
        self.mail = '*****@*****.**'
        self.fn   = './res/HIV_gp120.nex'
        self.datatype = 0
        self.gencodeid = 0
        self.type = 'meme'
        self.created_analysis = msa.upload_file(self.fn, self.datatype,
                                           self.gencodeid, self.mail)

        self.meme_params = {
            'treemode'    : 0,
            'modelstring' : '010010',
            'pvalue'      : 0.1,
            'sendmail'    : True
        }

        self.meme_analysis = analysis.create_analysis(self.created_analysis.id,
                                                      self.type,
                                                      self.meme_params)
Example #4
0
#  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.msa as msa
import datamonkey.analysis as analysis
import time

mail = '*****@*****.**'
fn   = './res/HIV_gp120.nex'

msa_obj = msa.upload_file(fn, 0, 0, mail)

bsrel_params = {
    'treemode'    : 0,
}

# Create a new analysis and poll
bsrel_analysis = analysis.create_analysis(msa_obj.id, 'bsrel', bsrel_params)
bsrel_analysis.poll()
print bsrel_analysis.json

## Get an existing analysis and print results
#bsrel_analysis = analysis.get_by_id(1, 'upload.958520133127023.1', 'bsrel' )
#results = bsrel_analysis.json['bsrelresults']
#print len(results)