--- /dev/null
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import os
+import tempfile
+import shutil
+import unittest
+
+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.test.simulate_runfolder import *
+
+
+def make_runfolder(obj=None):
+ """
+ Make a fake runfolder, attach all the directories to obj if defined
+ """
+ # make a fake runfolder directory
+ temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
+
+ 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)
+
+ ipar_dir = make_firecrest_dir(data_dir, "1.9.2", 1, 74)
+
+ matrix_dir = os.path.join(ipar_dir, 'Matrix')
+ os.mkdir(matrix_dir)
+ make_matrix(matrix_dir)
+
+ bustard_dir = os.path.join(ipar_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_summary_paired_htm(gerald_dir)
+ make_eland_multi(gerald_dir)
+
+ if obj is not None:
+ obj.temp_dir = temp_dir
+ obj.runfolder_dir = runfolder_dir
+ obj.data_dir = data_dir
+ obj.image_analysis_dir = ipar_dir
+ obj.matrix_dir = matrix_dir
+ obj.bustard_dir = bustard_dir
+ obj.gerald_dir = gerald_dir
+
+
+class RunfolderTests(unittest.TestCase):
+ """
+ Test components of the runfolder processing code
+ which includes firecrest, bustard, and gerald
+ """
+ def setUp(self):
+ # attaches all the directories to the object passed in
+ make_runfolder(self)
+
+ def tearDown(self):
+ shutil.rmtree(self.temp_dir)
+
+ def test_ipar(self):
+ """
+ Construct a firecrest object
+ """
+ i = ipar.ipar(self.image_analysis_dir)
+ self.failUnlessEqual(i.version, '2.01.192.0')
+ self.failUnlessEqual(i.start, 1)
+ self.failUnlessEqual(i.stop, 37)
+
+ xml = i.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+
+ i2 = ipar.IPAR(xml=xml)
+ self.failUnlessEqual(i.version, i2.version)
+ self.failUnlessEqual(i.start, i2.start)
+ self.failUnlessEqual(i.stop, i2.stop)
+ self.failUnlessEqual(i.date, i2.date)
+ self.failUnlessEqual(i.file_list(), i2.file_list())
+
+ def test_bustard(self):
+ """
+ construct a bustard object
+ """
+ b = bustard.bustard(self.bustard_dir)
+ 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(len(b.phasing), len(b2.phasing))
+ for key in b.phasing.keys():
+ self.failUnlessEqual(b.phasing[key].lane,
+ b2.phasing[key].lane)
+ self.failUnlessEqual(b.phasing[key].phasing,
+ b2.phasing[key].phasing)
+ 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)
+
+ 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(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
+ # 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', ]
+
+ # 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')
+ self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
+ self.failUnlessEqual(cur_lane.read_length, '32')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
+
+ # 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)
+
+ # 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))
+
+ xml = g.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+ g2 = gerald.Gerald(xml=xml)
+
+ # do it all again after extracting from the xml file
+ self.failUnlessEqual(g.version, g2.version)
+ self.failUnlessEqual(g.date, g2.date)
+ self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
+ self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+
+ # 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)]
+ 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])
+
+
+ def test_eland(self):
+ hg_map = {'Lambda.fa': 'Lambda.fa'}
+ for i in range(1,22):
+ short_name = 'chr%d.fa' % (i,)
+ 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 }
+ 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)
+ self.failUnlessEqual(lane.sample_name, "s")
+ self.failUnlessEqual(lane.lane_id, unicode(i))
+ self.failUnlessEqual(len(lane.mapped_reads), 15)
+ self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+ self.failUnlessEqual(lane.match_codes['U0'], 1)
+ 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()
+ # 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)]
+ 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])
+
+ 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_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ self.failUnlessEqual(runs[0].name, 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)
+
+ r1 = runs[0]
+ xml = r1.get_elements()
+ xml_str = ElementTree.tostring(xml)
+
+ r2 = runfolder.PipelineRun(xml=xml)
+ self.failUnlessEqual(r1.name, r2.name)
+ self.failIfEqual(r2.image_analysis, None)
+ self.failIfEqual(r2.bustard, None)
+ self.failIfEqual(r2.gerald, None)
+
+
+def suite():
+ return unittest.makeSuite(RunfolderTests,'test')
+
+if __name__ == "__main__":
+ unittest.main(defaultTest="suite")
+
projects / htsworkflow.git / commitdiff