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, paired=True)
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[i]
- self.failUnlessEqual(cur_lane.analysis, 'eland')
+ 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,
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[end].keys():
- g_results = g_eland.results[end][lane]
- g2_results = g_eland.results[end][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),
eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
# check first end
- for i in range(1,9):
- lane = eland.results[0][i]
- self.failUnlessEqual(lane.reads, 4)
+ 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, 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['QC'], 0)
# check second end
- for i in range(1,9):
- lane = eland.results[1][i]
- self.failUnlessEqual(lane.reads, 5)
+ 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, 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)
xml_str = ElementTree.tostring(xml)
e2 = gerald.ELAND(xml=xml)
- for end in [0, 1]:
- for i in range(1,9):
- l1 = eland.results[end][i]
- l2 = e2.results[end][i]
- 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)
- 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])
+ 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), 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])
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)
# firecrest's date depends on filename not the create time.
- name = 'run_207BTAAXX_2008-04-19.xml'
- self.failUnlessEqual(runs[0].name, name)
+ 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_2008-04-19.xml'
- 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