import shutil
import unittest
+from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import gerald
data_dir = os.path.join(runfolder_dir, 'Data')
os.mkdir(data_dir)
- ipar_dir = make_ipar_dir(data_dir)
+ ipar_dir = make_ipar_dir(data_dir, '1.30')
bustard_dir = os.path.join(ipar_dir,
'Bustard1.3.2_15-03-2008_diane')
os.mkdir(bustard_dir)
make_phasing_params(bustard_dir)
+ make_bustard_config132(bustard_dir)
gerald_dir = os.path.join(bustard_dir,
'GERALD_15-03-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(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
"""
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.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'])
+ check_crosstalk(b.crosstalk)
xml = b.get_elements()
b2 = bustard.Bustard(xml=xml)
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 1.68.2.2 2007/06/13 11:08:49 km Exp')
- self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
+ '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+ 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_results = g2_eland.results[0][lane]
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)
+ eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
- for i in range(1,9):
- lane = eland.results[0][i]
+ # 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(lane.match_codes['NM'], 1)
self.failUnlessEqual(lane.match_codes['QC'], 0)
- xml = eland.get_elements()
+ # 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)
+
+ 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]
+ l1 = eland_container.results[0][i]
l2 = e2.results[0][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), 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)