import os
import tempfile
import shutil
-import unittest
+from unittest import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines.eland import SampleKey
from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.test.simulate_runfolder import *
matrix_dir = os.path.join(ipar_dir, 'Matrix')
os.mkdir(matrix_dir)
- make_matrix(matrix_dir)
+ matrix_name = os.path.join(matrix_dir, 's_matrix.txt')
+ make_matrix(matrix_name)
bustard_dir = os.path.join(ipar_dir,
'Bustard1.8.28_12-04-2008_diane')
gerald_dir = os.path.join(bustard_dir,
'GERALD_12-04-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(gerald_dir)
+ make_gerald_config_100(gerald_dir)
make_summary_paired_htm(gerald_dir)
- make_eland_multi(gerald_dir)
+ make_eland_multi(gerald_dir, paired=True)
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
"""
f = firecrest.firecrest(self.image_analysis_dir)
+ self.failUnlessEqual(f.software, 'Firecrest')
self.failUnlessEqual(f.version, '1.9.6')
self.failUnlessEqual(f.start, 1)
self.failUnlessEqual(f.stop, 152)
self.failUnlessEqual(f.user, 'diane')
- # As of 2008-12-8, the date was being set in
+ # As of 2008-12-8, the date was being set in
# simulate_runfolder.make_firecrest_dir
self.failUnlessEqual(f.date, date(2008,4,12))
xml_str = ElementTree.tostring(xml)
f2 = firecrest.Firecrest(xml=xml)
+ self.failUnlessEqual(f.software, f2.software)
self.failUnlessEqual(f.version, f2.version)
self.failUnlessEqual(f.start, f2.start)
self.failUnlessEqual(f.stop, f2.stop)
construct a bustard object
"""
b = bustard.bustard(self.bustard_dir)
+ self.failUnlessEqual(b.software, 'Bustard')
self.failUnlessEqual(b.version, '1.8.28')
self.failUnlessEqual(b.date, date(2008,4,12))
self.failUnlessEqual(b.user, 'diane')
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)
# need to update gerald and make tests for it
g = gerald.gerald(self.gerald_dir)
- self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
- self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
+ 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/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
- '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
+ 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[str(i)]
- self.failUnlessEqual(cur_lane.analysis, 'eland')
+ 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, '32')
- self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
+ 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')
- self.failUnlessEqual(l.read_length, '32')
- self.failUnlessEqual(l.use_bases, 'Y'*32)
+ self.failUnlessEqual(l.analysis, 'eland_extended')
+ self.failUnlessEqual(l.read_length, '37')
+ self.failUnlessEqual(l.use_bases, 'Y'*37)
# test data extracted from summary file
- clusters = [None,
- (96483, 9074), (133738, 7938),
- (152142, 10002), (15784, 2162),
- (119735, 8465), (152177, 8146),
- (84649, 7325), (54622, 4812),]
-
- for i in range(1,9):
- summary_lane = g.summary[str(i)]
- self.failUnlessEqual(summary_lane.cluster, clusters[i])
- self.failUnlessEqual(summary_lane.lane, str(i))
+ clusters = [[None,
+ (103646, 4515), (106678, 4652),
+ (84583, 5963), (68813, 4782),
+ (104854, 4664), (43555, 1632),
+ (54265, 1588), (64363, 2697),],
+ [None,
+ (103647, 4516), (106679, 4653),
+ (84584, 5964), (68814, 4783),
+ (104855, 4665), (43556, 1633),
+ (54266, 1589), (64364, 2698),],]
+
+ for end in [0,1]:
+ for lane in range(1,9):
+ summary_lane = g.summary[end][lane]
+ self.failUnlessEqual(summary_lane.cluster, clusters[end][lane])
+ self.failUnlessEqual(summary_lane.lane, lane)
xml = g.get_elements()
# just make sure that element tree can serialize the tree
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()))
# test lane specific parameters from gerald config file
for i in range(1,9):
- g_lane = g.lanes[str(i)]
- g2_lane = g2.lanes[str(i)]
+ g_lane = g.lanes[i]
+ g2_lane = g2.lanes[i]
self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
# test (some) summary elements
- for i in range(1,9):
- g_summary = g.summary[str(i)]
- g2_summary = g2.summary[str(i)]
- self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
- self.failUnlessEqual(g_summary.lane, g2_summary.lane)
-
- g_eland = g.eland_results
- g2_eland = g2.eland_results
- for lane in g_eland.keys():
- self.failUnlessEqual(g_eland[lane].reads,
- g2_eland[lane].reads)
- self.failUnlessEqual(len(g_eland[lane].mapped_reads),
- len(g2_eland[lane].mapped_reads))
- for k in g_eland[lane].mapped_reads.keys():
- self.failUnlessEqual(g_eland[lane].mapped_reads[k],
- g2_eland[lane].mapped_reads[k])
-
- self.failUnlessEqual(len(g_eland[lane].match_codes),
- len(g2_eland[lane].match_codes))
- for k in g_eland[lane].match_codes.keys():
- self.failUnlessEqual(g_eland[lane].match_codes[k],
- g2_eland[lane].match_codes[k])
+ for end in [0,1]:
+ for i in range(1,9):
+ g_summary = g.summary[end][i]
+ g2_summary = g2.summary[end][i]
+ self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
+ self.failUnlessEqual(g_summary.lane, g2_summary.lane)
+
+ g_eland = g.eland_results
+ g2_eland = g2.eland_results
+ 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])
+
+ 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):
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 }
+ 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[str(i)]
- self.failUnlessEqual(lane.reads, 4)
+ # check first end
+ for key in eland.find_keys(SampleKey(read=1)):
+ lane = eland[key]
+ self.failUnlessEqual(lane.reads, 6)
self.failUnlessEqual(lane.sample_name, "s")
- self.failUnlessEqual(lane.lane_id, unicode(i))
- self.failUnlessEqual(len(lane.mapped_reads), 15)
+ 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'], 1)
+ 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['NM'], 1)
self.failUnlessEqual(lane.match_codes['QC'], 0)
+ # check second end
+ for key in eland.find_keys(SampleKey(read=2)):
+ lane = eland[key]
+ self.failUnlessEqual(lane.reads, 7)
+ 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'], 1)
+
xml = eland.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[str(i)]
- l2 = e2[str(i)]
+ for key in eland:
+ l1 = eland[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), 15)
+ self.failUnlessEqual(len(l1.mapped_reads), 17)
for k in l1.mapped_reads.keys():
self.failUnlessEqual(l1.mapped_reads[k],
l2.mapped_reads[k])
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
- name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
- self.failUnlessEqual(runs[0].name, name)
+ # firecrest's date depends on filename not the create time.
+ name = 'run_207BTAAXX_2009-02-22.xml'
+ 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)
+ name = 'run_207BTAAXY_2009-02-22.xml'
+ 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