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 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 *
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.image_analysis_dir = intensities_dir
obj.bustard_dir = unaligned_dir
obj.gerald_dir = aligned_dir
+ obj.reads = 2
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
def test_bustard(self):
"""Construct a bustard object"""
b = bustard.bustard(self.bustard_dir)
+ self.failUnlessEqual(b.software, 'RTA')
self.failUnlessEqual(b.version, '1.12.4.2')
self.failUnlessEqual(b.date, None)
self.failUnlessEqual(b.user, None)
xml = b.get_elements()
b2 = bustard.Bustard(xml=xml)
- self.failUnlessEqual(b.version, b2.version)
- self.failUnlessEqual(b.date, b2.date )
- self.failUnlessEqual(b.user, b2.user)
+ self.failUnlessEqual(b.software, b2.software)
+ self.failUnlessEqual(b.version, b2.version)
+ self.failUnlessEqual(b.date, b2.date )
+ self.failUnlessEqual(b.user, b2.user)
def test_gerald(self):
# need to update gerald and make tests for it
g = gerald.gerald(self.gerald_dir)
- self.failUnlessEqual(g.version, 'CASAVA-1.8.1')
+ 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()))
# make_gerald_config.
# the first None is to offset the genomes list to be 1..9
# instead of pythons default 0..8
- genomes = [None,
- '/g/mm9',
- '/g/mm9',
- '/g/elegans190',
- '/g/arabidopsis01222004',
- '/g/mm9',
- '/g/mm9',
- '/g/mm9',
- '/g/mm9', ]
-
# test lane specific parameters from gerald config file
- for i in range(1,9):
- cur_lane = g.lanes[i]
- self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
- self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
- self.failUnlessEqual(cur_lane.read_length, '37')
- self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
-
- # I want to be able to use a simple iterator
- for l in g.lanes.values():
- self.failUnlessEqual(l.analysis, 'eland_extended')
- self.failUnlessEqual(l.read_length, '37')
- self.failUnlessEqual(l.use_bases, 'Y'*37)
+
+ undetermined = g.lanes[SampleKey(sample='Undetermined_indices')]
+ self.failUnlessEqual(undetermined.analysis, 'none')
+ self.failUnlessEqual(undetermined.read_length, None)
+ self.failUnlessEqual(undetermined.use_bases, None)
+
+ project = g.lanes[SampleKey(sample='11115')]
+ self.failUnlessEqual(project.analysis, 'eland_extended')
+ self.failUnlessEqual(project.eland_genome, '/g/hg18/chromosomes/')
+ self.failUnlessEqual(project.read_length, '49')
+ self.failUnlessEqual(project.use_bases, 'y'*49+'n')
# test data extracted from summary file
clusters = [None,
- (281331, 11169), (203841, 13513),
- (220889, 15653), (137294, 14666),
- (129388, 14525), (262092, 10751),
- (185754, 13503), (233765, 9537),]
+ (3878755, 579626.0), (3920639, 1027332.4),
+ (5713049, 876187.3), (5852907, 538640.6),
+ (4006751, 1265247.4), (5678021, 627070.7),
+ (1854131, 429053.2), (4777517, 592904.0),
+ ]
- self.failUnlessEqual(len(g.summary), 1)
+ self.failUnlessEqual(len(g.summary), self.reads)
for i in range(1,9):
summary_lane = g.summary[0][i]
self.failUnlessEqual(summary_lane.cluster, clusters[i])
xml = g.get_elements()
# just make sure that element tree can serialize the tree
xml_str = ElementTree.tostring(xml)
- g2 = gerald.Gerald(xml=xml)
- return
+ g2 = gerald.CASAVA(xml=xml)
# do it all again after extracting from the xml file
+ 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()))
# test lane specific parameters from gerald config file
- for i in range(1,9):
+ for i in g.lanes.keys():
g_lane = g.lanes[i]
g2_lane = g2.lanes[i]
self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
# test (some) summary elements
- self.failUnlessEqual(len(g.summary), 1)
+ self.failUnlessEqual(len(g.summary), self.reads)
for i in range(1,9):
g_summary = g.summary[0][i]
g2_summary = g2.summary[0][i]
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):
def test_eland(self):
- return
hg_map = {'Lambda.fa': 'Lambda.fa'}
for i in range(1,22):
short_name = 'chr%d.fa' % (i,)
long_name = 'hg18/chr%d.fa' % (i,)
hg_map[short_name] = long_name
- genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
- 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
+ samples = set(('11111', '11112', '11113', '11114', '11115',
+ '11116', '11117', '11118', '11119', '11120'))
+ genome_maps = {}
+ for i in range(1,9):
+ genome_maps[i] = hg_map
+
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 lane in 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)
+ self.assertEqual(lane.mapped_reads['hg18/chr9.fa'], 6)
+ self.assertEqual(lane.match_codes['U0'], 6)
+ self.assertEqual(lane.match_codes['R0'], 18)
+ self.assertEqual(lane.match_codes['R1'], 24)
+ self.assertEqual(lane.match_codes['R2'], 18)
+ self.assertEqual(lane.match_codes['NM'], 12)
+ else:
+ self.assertEqual(lane.reads, 8)
+ self.assertEqual(lane.mapped_reads['hg18/chr9.fa'], 2)
+ self.assertEqual(lane.match_codes['U0'], 2)
+ self.assertEqual(lane.match_codes['R0'], 6)
+ self.assertEqual(lane.match_codes['R1'], 8)
+ self.assertEqual(lane.match_codes['R2'], 6)
+ self.assertEqual(lane.match_codes['NM'], 4)
+
+ self.assertTrue(lane.sample_name in samples)
+ #self.assertEqual(lane.lane_id, 1)
+ self.assertEqual(len(lane.mapped_reads), 1)
+ self.assertEqual(lane.match_codes['U1'], 0)
+ self.assertEqual(lane.match_codes['U2'], 0)
+ self.assertEqual(lane.match_codes['QC'], 0)
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.results:
+ l1 = eland_container.results[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)
+ self.failUnlessEqual(len(l1.mapped_reads), 1)
for k in l1.mapped_reads.keys():
self.failUnlessEqual(l1.mapped_reads[k],
l2.mapped_reads[k])
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