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 *
os.mkdir(gerald_dir)
make_gerald_config_100(gerald_dir)
make_summary_ipar130_htm(gerald_dir)
- make_eland_multi(gerald_dir)
+ make_eland_multi(gerald_dir, lane_list=[1,2,3,4,5,6,])
+ make_scarf(gerald_dir, lane_list=[7,])
+ make_fastq(gerald_dir, lane_list=[8,])
if obj is not None:
obj.temp_dir = temp_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
Construct a firecrest object
"""
i = ipar.ipar(self.image_analysis_dir)
+ self.failUnlessEqual(i.software, 'IPAR')
self.failUnlessEqual(i.version, '2.01.192.0')
self.failUnlessEqual(i.start, 1)
self.failUnlessEqual(i.stop, 37)
xml_str = ElementTree.tostring(xml)
i2 = ipar.IPAR(xml=xml)
+ self.failUnlessEqual(i.software, i2.software)
self.failUnlessEqual(i.version, i2.version)
self.failUnlessEqual(i.start, i2.start)
self.failUnlessEqual(i.stop, i2.stop)
"""
construct a bustard object
"""
+ def check_crosstalk(crosstalk):
+ self.failUnlessAlmostEqual(crosstalk.base['A'][0], 1.27)
+ self.failUnlessAlmostEqual(crosstalk.base['A'][1], 0.20999999999999)
+ self.failUnlessAlmostEqual(crosstalk.base['A'][2], -0.02)
+ self.failUnlessAlmostEqual(crosstalk.base['A'][3], -0.03)
+
+ self.failUnlessAlmostEqual(crosstalk.base['C'][0], 0.57)
+ self.failUnlessAlmostEqual(crosstalk.base['C'][1], 0.58)
+ self.failUnlessAlmostEqual(crosstalk.base['C'][2], -0.01)
+ self.failUnlessAlmostEqual(crosstalk.base['C'][3], -0.01)
+
+ self.failUnlessAlmostEqual(crosstalk.base['T'][0], -0.02)
+ self.failUnlessAlmostEqual(crosstalk.base['T'][1], -0.02)
+ self.failUnlessAlmostEqual(crosstalk.base['T'][2], 0.80)
+ self.failUnlessAlmostEqual(crosstalk.base['T'][3], 1.07)
+
+ self.failUnlessAlmostEqual(crosstalk.base['G'][0], -0.03)
+ self.failUnlessAlmostEqual(crosstalk.base['G'][1], -0.04)
+ self.failUnlessAlmostEqual(crosstalk.base['G'][2], 1.51)
+ self.failUnlessAlmostEqual(crosstalk.base['G'][3], -0.02)
+
b = bustard.bustard(self.bustard_dir)
+ self.failUnlessEqual(b.software, 'Bustard')
self.failUnlessEqual(b.version, '1.3.2')
self.failUnlessEqual(b.date, date(2008,3,15))
self.failUnlessEqual(b.user, 'diane')
self.failUnlessEqual(len(b.phasing), 8)
self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
self.failUnlessEqual(b.crosstalk.base.keys(), ['A','C','T','G'])
-
- self.failUnlessAlmostEqual(b.crosstalk.base['A'][0], 1.27)
- self.failUnlessAlmostEqual(b.crosstalk.base['A'][1], 0.20999999999999)
- self.failUnlessAlmostEqual(b.crosstalk.base['A'][2], -0.02)
- self.failUnlessAlmostEqual(b.crosstalk.base['A'][3], -0.03)
-
- self.failUnlessAlmostEqual(b.crosstalk.base['C'][0], 0.57)
- self.failUnlessAlmostEqual(b.crosstalk.base['C'][1], 0.58)
- self.failUnlessAlmostEqual(b.crosstalk.base['C'][2], -0.01)
- self.failUnlessAlmostEqual(b.crosstalk.base['C'][3], -0.01)
-
- self.failUnlessAlmostEqual(b.crosstalk.base['T'][0], -0.02)
- self.failUnlessAlmostEqual(b.crosstalk.base['T'][1], -0.02)
- self.failUnlessAlmostEqual(b.crosstalk.base['T'][2], 0.80)
- self.failUnlessAlmostEqual(b.crosstalk.base['T'][3], 1.07)
-
- self.failUnlessAlmostEqual(b.crosstalk.base['G'][0], -0.03)
- self.failUnlessAlmostEqual(b.crosstalk.base['G'][1], -0.04)
- self.failUnlessAlmostEqual(b.crosstalk.base['G'][2], 1.51)
- self.failUnlessAlmostEqual(b.crosstalk.base['G'][3], -0.02)
+ check_crosstalk(b.crosstalk)
xml = b.get_elements()
b2 = bustard.Bustard(xml=xml)
+ self.failUnlessEqual(b.software, b2.software)
self.failUnlessEqual(b.version, b2.version)
self.failUnlessEqual(b.date, b2.date )
self.failUnlessEqual(b.user, b2.user)
b2.phasing[key].phasing)
self.failUnlessEqual(b.phasing[key].prephasing,
b2.phasing[key].prephasing)
+ check_crosstalk(b2.crosstalk)
def test_gerald(self):
# need to update gerald and make tests for it
g = gerald.gerald(self.gerald_dir)
- self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+ 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()))
# 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',
+ genomes = [None,
+ '/g/mm9',
+ '/g/mm9',
+ '/g/elegans190',
'/g/arabidopsis01222004',
- '/g/mm9',
- '/g/mm9',
- '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
'/g/mm9', ]
# test lane specific parameters from gerald config file
g2 = gerald.Gerald(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()))
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)
- self.failUnlessEqual(len(g_results.mapped_reads),
- len(g2_results.mapped_reads))
- for k in g_results.mapped_reads.keys():
- self.failUnlessEqual(g_results.mapped_reads[k],
- g2_results.mapped_reads[k])
+ 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():
+ 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():
- self.failUnlessEqual(g_results.match_codes[k],
- g2_results.match_codes[k])
+ self.failUnlessEqual(len(g_results.match_codes),
+ len(g2_results.match_codes))
+ for k in g_results.match_codes.keys():
+ self.failUnlessEqual(g_results.match_codes[k],
+ g2_results.match_codes[k])
def test_eland(self):
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 }
- eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
-
- for i in range(1,9):
- lane = eland.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)
-
- xml = eland.get_elements()
+ 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 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.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)
- 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(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():
- self.failUnlessEqual(l1.match_codes[k],
- l2.match_codes[k])
+ 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(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():
+ 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):
runs = runfolder.get_runs(self.runfolder_dir)
# 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