From bb149aff8b5f9c748d656e35edd6667c5e7ec490 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 3 Dec 2008 22:24:29 +0000 Subject: [PATCH] Add test code to see if runfolder can handle something that looks like a paired end run. --- .../pipelines/test/test_runfolder_pair.py | 287 ++++++++++++++++++ 1 file changed, 287 insertions(+) create mode 100644 htsworkflow/pipelines/test/test_runfolder_pair.py diff --git a/htsworkflow/pipelines/test/test_runfolder_pair.py b/htsworkflow/pipelines/test/test_runfolder_pair.py new file mode 100644 index 0000000..e5997b7 --- /dev/null +++ b/htsworkflow/pipelines/test/test_runfolder_pair.py @@ -0,0 +1,287 @@ +#!/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") + -- 2.30.2