import os
import tempfile
import shutil
-import unittest
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
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 *
obj.gerald_dir = gerald_dir
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
g_eland = g.eland_results
g2_eland = g2.eland_results
- for lane in g_eland.results[0].keys():
- g_results = g_eland.results[0][lane]
- g2_results = g2_eland.results[0][lane]
+ for key in g_eland:
+ g_results = g_eland[key]
+ g2_results = g2_eland[key]
self.failUnlessEqual(g_results.reads,
g2_results.reads)
if isinstance(g_results, eland.ElandLane):
eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
# I added sequence lanes to the last 2 lanes of this test case
- for i in range(1,7):
- lane = eland_container.results[0][i]
- self.failUnlessEqual(lane.reads, 6)
- self.failUnlessEqual(lane.sample_name, "s")
- self.failUnlessEqual(lane.lane_id, i)
- self.failUnlessEqual(len(lane.mapped_reads), 17)
- self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
- self.failUnlessEqual(lane.match_codes['U0'], 3)
- self.failUnlessEqual(lane.match_codes['R0'], 2)
- self.failUnlessEqual(lane.match_codes['U1'], 1)
- self.failUnlessEqual(lane.match_codes['R1'], 9)
- self.failUnlessEqual(lane.match_codes['U2'], 0)
- self.failUnlessEqual(lane.match_codes['R2'], 12)
- self.failUnlessEqual(lane.match_codes['NM'], 1)
- self.failUnlessEqual(lane.match_codes['QC'], 0)
-
- # test scarf
- lane = eland_container.results[0][7]
- self.failUnlessEqual(lane.reads, 5)
- self.failUnlessEqual(lane.sample_name, 's')
- self.failUnlessEqual(lane.lane_id, 7)
- self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
-
- # test fastq
- lane = eland_container.results[0][8]
- self.failUnlessEqual(lane.reads, 3)
- self.failUnlessEqual(lane.sample_name, 's')
- self.failUnlessEqual(lane.lane_id, 8)
- self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
+ for key in eland_container:
+ lane = eland_container[key]
+ if key.lane in [1,2,3,4,5,6]:
+ self.failUnlessEqual(lane.reads, 6)
+ self.failUnlessEqual(lane.sample_name, "s")
+ self.failUnlessEqual(lane.lane_id, key.lane)
+ self.failUnlessEqual(len(lane.mapped_reads), 17)
+ self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+ self.failUnlessEqual(lane.match_codes['U0'], 3)
+ self.failUnlessEqual(lane.match_codes['R0'], 2)
+ self.failUnlessEqual(lane.match_codes['U1'], 1)
+ self.failUnlessEqual(lane.match_codes['R1'], 9)
+ self.failUnlessEqual(lane.match_codes['U2'], 0)
+ self.failUnlessEqual(lane.match_codes['R2'], 12)
+ self.failUnlessEqual(lane.match_codes['NM'], 1)
+ self.failUnlessEqual(lane.match_codes['QC'], 0)
+ elif key.lane == 7:
+ self.failUnlessEqual(lane.reads, 5)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 7)
+ self.failUnlessEqual(lane.sequence_type,
+ eland.SequenceLane.SCARF_TYPE)
+ elif key.lane == 8:
+ self.failUnlessEqual(lane.reads, 3)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 8)
+ self.failUnlessEqual(lane.sequence_type,
+ eland.SequenceLane.FASTQ_TYPE)
xml = eland_container.get_elements()
# just make sure that element tree can serialize the tree
xml_str = ElementTree.tostring(xml)
e2 = gerald.ELAND(xml=xml)
- for i in range(1,9):
- l1 = eland_container.results[0][i]
- l2 = e2.results[0][i]
+ for key in eland_container:
+ l1 = eland_container[key]
+ l2 = e2[key]
self.failUnlessEqual(l1.reads, l2.reads)
self.failUnlessEqual(l1.sample_name, l2.sample_name)
self.failUnlessEqual(l1.lane_id, l2.lane_id)
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
name = 'run_3021JAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
- self.failUnlessEqual(runs[0].name, name)
+ self.failUnlessEqual(runs[0].serialization_filename, 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.failUnlessEqual(runs[0].serialization_filename, name)
r1 = runs[0]
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__":
- unittest.main(defaultTest="suite")
+if __name__ == "__main__":
+ from unittest import main
+ main(defaultTest="suite")
projects / htsworkflow.git / blobdiff