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.samplekey import SampleKey
+from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.test.simulate_runfolder import *
# make a fake runfolder directory
temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
- runfolder_dir = os.path.join(temp_dir,
- '090608_HWI-EAS229_0117_4286GAAXX')
+ flowcell_id = '4286GAAXX'
+ runfolder_dir = os.path.join(
+ temp_dir,
+ '090608_HWI-EAS229_0117_{0}'.format(flowcell_id))
os.mkdir(runfolder_dir)
data_dir = os.path.join(runfolder_dir, 'Data')
make_fastq(gerald_dir, lane_list=[8,])
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.gerald_dir = gerald_dir
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
self.failUnlessEqual(g.software, 'GERALD')
self.failUnlessEqual(g.version, '1.171')
self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
- 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
self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
# I want to be able to use a simple iterator
- for l in g.lanes.values():
+ for l in list(g.lanes.values()):
self.failUnlessEqual(l.analysis, 'eland_extended')
self.failUnlessEqual(l.read_length, '37')
self.failUnlessEqual(l.use_bases, 'Y'*37)
# just make sure that element tree can serialize the tree
xml_str = ElementTree.tostring(xml)
g2 = gerald.Gerald(xml=xml)
- return
# do it all again after extracting from the xml file
- self.failUnlessEqual(g.software, g2.version)
+ 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 range(1,9):
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 lane in g_eland:
+ g_results = g_eland[lane]
+ g2_results = g2_eland[lane]
self.failUnlessEqual(g_results.reads,
g2_results.reads)
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])
def test_eland(self):
- return
hg_map = {'Lambda.fa': 'Lambda.fa'}
for i in range(1,22):
short_name = 'chr%d.fa' % (i,)
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)
+ keys = [SampleKey(lane=i, read=1, sample='s') for i in range(1,7)]
+ for key in keys:
+ lane = eland_container[key]
+ self.failUnlessEqual(lane.reads, 28)
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.lane_id, key.lane)
+ self.failUnlessEqual(len(lane.mapped_reads), 7)
+ self.failUnlessEqual(lane.mapped_reads['hg18/chr7.fa'], 4)
+ self.failUnlessEqual(lane.mapped_reads['Lambda_1-1_11936nts.fa'], 1)
+ self.failUnlessEqual(lane.match_codes['U0'], 1)
+ self.failUnlessEqual(lane.match_codes['R0'], 20)
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)
+ self.failUnlessEqual(lane.match_codes['R1'], 2)
+ self.failUnlessEqual(lane.match_codes['U2'], 11)
+ self.failUnlessEqual(lane.match_codes['R2'], 0)
+ self.failUnlessEqual(lane.match_codes['NM'], 2)
+ self.failUnlessEqual(lane.match_codes['QC'], 9)
# test scarf
- lane = eland_container.results[0][7]
+ lane = eland_container[SampleKey(lane=7, read=1, sample='s')]
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]
+ lane = eland_container[SampleKey(lane=8, read=1, sample='s')]
self.failUnlessEqual(lane.reads, 3)
self.failUnlessEqual(lane.sample_name, 's')
self.failUnlessEqual(lane.lane_id, 8)
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.results[key]
self.failUnlessEqual(l1.reads, l2.reads)
self.failUnlessEqual(l1.sample_name, l2.sample_name)
self.failUnlessEqual(l1.lane_id, l2.lane_id)
if isinstance(l1, eland.ElandLane):
self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
- self.failUnlessEqual(len(l1.mapped_reads), 17)
- for k in l1.mapped_reads.keys():
+ self.failUnlessEqual(len(l1.mapped_reads), 7)
+ 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)
+ 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