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 import runfolder
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.test.simulate_runfolder import *
-
+
def make_summary_htm(gerald_dir):
summary_htm="""<!--RUN_TIME Wed Jul 2 06:47:44 2008 -->
<!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
>HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
"""
for i in range(1,9):
- pathname = os.path.join(gerald_dir,
+ pathname = os.path.join(gerald_dir,
's_%d_eland_result.txt' % (i,))
f = open(pathname, 'w')
f.write(eland_result)
# make a fake runfolder directory
temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
- runfolder_dir = os.path.join(temp_dir,
+ runfolder_dir = os.path.join(temp_dir,
'080102_HWI-EAS229_0010_207BTAAXX')
os.mkdir(runfolder_dir)
data_dir = os.path.join(runfolder_dir, 'Data')
os.mkdir(data_dir)
- firecrest_dir = os.path.join(data_dir,
+ firecrest_dir = os.path.join(data_dir,
'C1-33_Firecrest1.8.28_12-04-2008_diane'
)
os.mkdir(firecrest_dir)
matrix_dir = os.path.join(firecrest_dir, 'Matrix')
os.mkdir(matrix_dir)
- make_matrix(matrix_dir)
+ matrix_filename = os.path.join(matrix_dir, 's_matrix.txt')
+ make_matrix(matrix_filename)
- bustard_dir = os.path.join(firecrest_dir,
+ bustard_dir = os.path.join(firecrest_dir,
'Bustard1.8.28_12-04-2008_diane')
os.mkdir(bustard_dir)
make_phasing_params(bustard_dir)
gerald_dir = os.path.join(bustard_dir,
'GERALD_12-04-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(gerald_dir)
+ make_gerald_config_026(gerald_dir)
make_summary_htm(gerald_dir)
make_eland_results(gerald_dir)
obj.matrix_dir = matrix_dir
obj.bustard_dir = bustard_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.firecrest_dir)
+ self.failUnlessEqual(f.software, 'Firecrest')
self.failUnlessEqual(f.version, '1.8.28')
self.failUnlessEqual(f.start, 1)
self.failUnlessEqual(f.stop, 33)
xml_str = ElementTree.tostring(xml)
f2 = firecrest.Firecrest(xml=xml)
- self.failUnlessEqual(f.version, f2.version)
- self.failUnlessEqual(f.start, f2.start)
- self.failUnlessEqual(f.stop, f2.stop)
- self.failUnlessEqual(f.user, f2.user)
- self.failUnlessEqual(f.date, f2.date)
+ self.failUnlessEqual(f.software, f2.software)
+ self.failUnlessEqual(f.version, f2.version)
+ self.failUnlessEqual(f.start, f2.start)
+ self.failUnlessEqual(f.stop, f2.stop)
+ self.failUnlessEqual(f.user, f2.user)
+ self.failUnlessEqual(f.date, f2.date)
def test_bustard(self):
"""
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')
self.failUnlessEqual(len(b.phasing), 8)
self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
-
+
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)
self.failUnlessEqual(len(b.phasing), len(b2.phasing))
for key in b.phasing.keys():
- self.failUnlessEqual(b.phasing[key].lane,
+ self.failUnlessEqual(b.phasing[key].lane,
b2.phasing[key].lane)
- self.failUnlessEqual(b.phasing[key].phasing,
+ self.failUnlessEqual(b.phasing[key].phasing,
b2.phasing[key].phasing)
- self.failUnlessEqual(b.phasing[key].prephasing,
+ self.failUnlessEqual(b.phasing[key].prephasing,
b2.phasing[key].prephasing)
def test_gerald(self):
# need to update gerald and make tests for it
- g = gerald.gerald(self.gerald_dir)
+ 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.software, 'GERALD')
+ self.failUnlessEqual(g.version, '1.68.2.2')
self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
-
- # list of genomes, matches what was defined up in
+
+ # list of genomes, matches what was defined up in
# make_gerald_config.
# the first None is to offset the genomes list to be 1..9
# instead of pythons default 0..8
self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
# test data extracted from summary file
- clusters = [None,
- (96483, 9074), (133738, 7938),
- (152142, 10002), (15784, 2162),
+ clusters = [None,
+ (96483, 9074), (133738, 7938),
+ (152142, 10002), (15784, 2162),
(119735, 8465), (152177, 8146),
(84649, 7325), (54622, 4812),]
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 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):
genome_maps = { 1:dm3_map, 2:dm3_map, 3:dm3_map, 4:dm3_map,
5:dm3_map, 6:dm3_map, 7:dm3_map, 8:dm3_map }
eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
-
- for i in range(1,9):
- lane = eland[i]
+
+ for key in eland:
+ lane = eland[key]
self.failUnlessEqual(lane.reads, 4)
self.failUnlessEqual(lane.sample_name, "s")
- self.failUnlessEqual(lane.lane_id, i)
+ self.failUnlessEqual(lane.lane_id, key.lane)
self.failUnlessEqual(len(lane.mapped_reads), 3)
self.failUnlessEqual(lane.mapped_reads['Lambda.fa'], 1)
self.failUnlessEqual(lane.mapped_reads['dm3/chr2L.fa'], 1)
xml_str = ElementTree.tostring(xml)
e2 = gerald.ELAND(xml=xml)
- for i in range(1,9):
- l1 = eland[i]
- l2 = e2[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.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],
+ self.failUnlessEqual(l1.match_codes[k],
l2.match_codes[k])
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)
- self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml')
+ self.failUnlessEqual(runs[0].serialization_filename, 'run_207BTAAXX_2008-04-19.xml')
# 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)
- self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml')
-
+ self.failUnlessEqual(runs[0].serialization_filename, 'run_207BTAAXY_2008-04-19.xml')
+
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")
-
+ from unittest import main
+ main(defaultTest="suite")
projects / htsworkflow.git / blobdiff