import os
import tempfile
import shutil
-import unittest
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.test.simulate_runfolder import *
flowcell_id = 'D07K6ACXX'
temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
- runfolder_dir = os.path.join(temp_dir,
- '110815_SN787_0101_A{0}'.format(flowcell_id))
+ runfolder_dir = os.path.join(
+ temp_dir,
+ '110815_SN787_0101_A{0}'.format(flowcell_id))
os.mkdir(runfolder_dir)
+ make_runinfo(runfolder_dir, flowcell_id)
+
data_dir = os.path.join(runfolder_dir, 'Data')
os.mkdir(data_dir)
os.mkdir(unaligned_dir)
make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id)
make_unaligned_config_1_12(unaligned_dir)
+ make_unaligned_status_1_12(unaligned_dir, flowcell_id)
aligned_dir = os.path.join(runfolder_dir, "Aligned")
os.mkdir(aligned_dir)
make_aligned_config_1_12(aligned_dir)
if obj is not None:
+ obj.flowcell_id = flowcell_id
obj.temp_dir = temp_dir
obj.runfolder_dir = runfolder_dir
obj.data_dir = data_dir
obj.reads = 2
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
self.failUnlessEqual(g.software, 'CASAVA')
self.failUnlessEqual(g.version, '1.8.1')
- self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
- self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+ self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+ self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))
# list of genomes, matches what was defined up in
# make_gerald_config.
self.failUnlessEqual(g.software, g2.software)
self.failUnlessEqual(g.version, g2.version)
self.failUnlessEqual(g.date, g2.date)
- self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
- self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+ self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+ self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))
# test lane specific parameters from gerald config file
- for i in g.lanes.keys():
+ for i in list(g.lanes.keys()):
g_lane = g.lanes[i]
g2_lane = g2.lanes[i]
self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
if isinstance(g_results, eland.ElandLane):
self.failUnlessEqual(len(g_results.mapped_reads),
len(g2_results.mapped_reads))
- for k in g_results.mapped_reads.keys():
+ for k in list(g_results.mapped_reads.keys()):
self.failUnlessEqual(g_results.mapped_reads[k],
g2_results.mapped_reads[k])
self.failUnlessEqual(len(g_results.match_codes),
len(g2_results.match_codes))
- for k in g_results.match_codes.keys():
+ for k in list(g_results.match_codes.keys()):
self.failUnlessEqual(g_results.match_codes[k],
g2_results.match_codes[k])
eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
- for lane in eland_container.values():
+ for lane in list(eland_container.values()):
# I added sequence lanes to the last 2 lanes of this test case
if lane.sample_name == '11113':
self.assertEqual(lane.reads, 24)
if isinstance(l1, eland.ElandLane):
self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
self.failUnlessEqual(len(l1.mapped_reads), 1)
- for k in l1.mapped_reads.keys():
+ for k in list(l1.mapped_reads.keys()):
self.failUnlessEqual(l1.mapped_reads[k],
l2.mapped_reads[k])
self.failUnlessEqual(len(l1.match_codes), 9)
self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
- for k in l1.match_codes.keys():
+ for k in list(l1.match_codes.keys()):
self.failUnlessEqual(l1.match_codes[k],
l2.match_codes[k])
elif isinstance(l1, eland.SequenceLane):
self.failUnlessEqual(l1.sequence_type, l2.sequence_type)
def test_runfolder(self):
- return
runs = runfolder.get_runs(self.runfolder_dir)
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
- name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
- self.failUnlessEqual(runs[0].name, name)
-
- # do we get the flowcell id from the FlowcellId.xml file
- make_flowcell_id(self.runfolder_dir, '207BTAAXY')
- runs = runfolder.get_runs(self.runfolder_dir)
- self.failUnlessEqual(len(runs), 1)
- name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
- self.failUnlessEqual(runs[0].name, name)
+ self.assertEqual(runs[0].flowcell_id, self.flowcell_id)
+ name = 'run_%s_%s.xml' % ( self.flowcell_id,
+ date.today().strftime('%Y-%m-%d'),)
+ self.failUnlessEqual(runs[0].serialization_filename, name)
+ bustard_dir = os.path.join(self.runfolder_dir, 'Unaligned')
r1 = runs[0]
+ self.failUnlessEqual(r1.bustard.sequence_format, 'fastq')
+ self.failUnlessEqual(r1.bustard.pathname, bustard_dir)
+ self.failUnlessEqual(r1.gerald.runfolder_name, 'Unaligned')
+
xml = r1.get_elements()
xml_str = ElementTree.tostring(xml)
r2 = runfolder.PipelineRun(xml=xml)
- self.failUnlessEqual(r1.name, r2.name)
+ self.failUnlessEqual(r1.serialization_filename, r2.serialization_filename)
self.failIfEqual(r2.image_analysis, None)
self.failIfEqual(r2.bustard, None)
self.failIfEqual(r2.gerald, None)
-
def suite():
- return unittest.makeSuite(RunfolderTests,'test')
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+ return suite
-if __name__ == "__main__":
- logging.basicConfig(level=logging.WARN)
- unittest.main(defaultTest="suite")
+if __name__ == "__main__":
+ from unittest import main
+ main(defaultTest="suite")
projects / htsworkflow.git / blobdiff