From 02cae8613181bb32f9a63a419a75b37216f34dfa Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 29 Feb 2012 16:58:39 -0800 Subject: [PATCH] Simulate a HiSeq runfolder. Also man do i need to clean up my simulation code --- .../pipelines/test/simulate_runfolder.py | 246 +- .../pipelines/test/test_runfolder_rta1_12.py | 291 ++ .../test/testdata/aligned_config_1_12.xml | 234 ++ .../test/testdata/demultiplex_1.12.4.2.xml | 71 + .../demultiplexed_bustard_1.12.4.2.xml | 503 +++ .../demultiplexed_summary_1.12.4.2.xml | 3669 +++++++++++++++++ .../rta_basecalls_config_1.12.4.2.xml | 511 +++ .../rta_intensities_config_1.12.4.2.xml | 472 +++ .../test/testdata/sample_summary_1_12.htm | 434 ++ 9 files changed, 6430 insertions(+), 1 deletion(-) create mode 100644 htsworkflow/pipelines/test/test_runfolder_rta1_12.py create mode 100644 htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml create mode 100644 htsworkflow/pipelines/test/testdata/demultiplex_1.12.4.2.xml create mode 100644 htsworkflow/pipelines/test/testdata/demultiplexed_bustard_1.12.4.2.xml create mode 100644 htsworkflow/pipelines/test/testdata/demultiplexed_summary_1.12.4.2.xml create mode 100755 htsworkflow/pipelines/test/testdata/rta_basecalls_config_1.12.4.2.xml create mode 100755 htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml create mode 100644 htsworkflow/pipelines/test/testdata/sample_summary_1_12.htm diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py index c07783e..0b57631 100644 --- a/htsworkflow/pipelines/test/simulate_runfolder.py +++ b/htsworkflow/pipelines/test/simulate_runfolder.py @@ -1,7 +1,7 @@ """ Create simulated solexa/illumina runfolders for testing """ - +import gzip import os import shutil @@ -55,6 +55,25 @@ def make_bustard_config132(image_dir): destination = os.path.join(image_dir, 'config.xml') shutil.copy(source, destination) +def make_aligned_config_1_12(aligned_dir): + """This is rouglhly equivalent to the old gerald file""" + source = os.path.join(TESTDATA_DIR, 'aligned_config_1_12.xml') + destination = os.path.join(aligned_dir, 'config.xml') + shutil.copy(source, destination) + +def make_unaligned_config_1_12(unaligned_dir): + demultiplex_pairs = [ # (src, + # dest), + (os.path.join(TESTDATA_DIR, 'demultiplex_1.12.4.2.xml'), + os.path.join(unaligned_dir, 'DemultiplexConfig.xml')), + (os.path.join(TESTDATA_DIR, 'demultiplexed_bustard_1.12.4.2.xml'), + os.path.join(unaligned_dir, 'DemultiplexConfig.xml')), + (os.path.join(TESTDATA_DIR, 'demultiplexed_summary_1.12.4.2.xml'), + os.path.join(unaligned_dir, 'DemultiplexConfig.xml')), + ] + for src, dest in demultiplex_pairs: + shutil.copy(src, dest) + def make_rta_intensities_1460(data_dir, version='1.4.6.0'): """ Construct an artificial RTA Intensities parameter file and directory @@ -107,6 +126,19 @@ def make_rta_intensities_1_10(data_dir, version='1.10.36.0'): return intensities_dir +def make_rta_intensities_1_12(data_dir, version='1.12.4.2'): + """ + Construct an artificial RTA Intensities parameter file and directory + """ + intensities_dir = os.path.join(data_dir, 'Intensities') + if not os.path.exists(intensities_dir): + os.mkdir(intensities_dir) + + param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.12.4.2.xml') + shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml')) + + return intensities_dir + def make_rta_basecalls_1870(intensities_dir): """ Construct an artificial RTA Intensities parameter file and directory @@ -134,6 +166,21 @@ def make_rta_basecalls_1_10(intensities_dir): return basecalls_dir +def make_rta_basecalls_1_12(intensities_dir): + """ + Construct an artificial RTA Intensities parameter file and directory + """ + basecalls_dir = os.path.join(intensities_dir, 'BaseCalls') + if not os.path.exists(basecalls_dir): + os.mkdir(basecalls_dir) + + make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO) + param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.12.4.2.xml') + shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml')) + + return basecalls_dir + + def make_qseqs(bustard_dir, basecall_info=None): """ Fill gerald directory with qseq files @@ -234,6 +281,9 @@ def make_matrix_dir_rta160(bustard_dir): def make_matrix_dir_rta_1_10(bustard_dir): make_matrix_dir_rta160(bustard_dir) +def make_matrix_dir_rta_1_12(bustard_dir): + make_matrix_dir_rta160(bustard_dir) + def make_phasing_dir(bustard_dir): """ Create several phasing files in /Phasing/ @@ -394,6 +444,200 @@ _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa f.write(seq) f.close() +UNALIGNED_READS = [1,2] +UNALIGNED_SAMPLES = [ (1, UNALIGNED_READS, '11111', None, None), + (2, UNALIGNED_READS, '11112', None, None), + (3, UNALIGNED_READS, '11113', 1, 'ATCACG'), + (3, UNALIGNED_READS, '11113', 2, 'CGATGT'), + (3, UNALIGNED_READS, '11113', 3, 'TTAGGC'), + (4, UNALIGNED_READS, '11114', 6, 'GCCAAT'), + (5, UNALIGNED_READS, '11115', 1, 'ATCACG'), + (5, UNALIGNED_READS, '11116', 7, 'ACTTGA'), + (5, UNALIGNED_READS, '11117', 9, 'GATCAG'), + (6, UNALIGNED_READS, '11118', 1, 'ATCACG'), + (7, UNALIGNED_READS, '11119', 2, 'CGATGT'), + (8, UNALIGNED_READS, '11120', 3, 'TTAGGC'), + (1, UNALIGNED_READS, None, None, None), + (2, UNALIGNED_READS, None, None, None), + (3, UNALIGNED_READS, None, None, None), + (4, UNALIGNED_READS, None, None, None), + (5, UNALIGNED_READS, None, None, None)] + + +def make_aligned_eland_export(aligned_dir, flowcell_id): + summary_source = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm') + for lane, read, project_id, index_id, index_seq in UNALIGNED_SAMPLES: + paths = DemultiplexedPaths(aligned_dir, + flowcell_id, + lane, + project_id, + index_id, + index_seq) + paths.make_sample_dirs() + paths.make_summary_dirs() + summary_dest = os.path.join(paths.summary_dir, 'Sample_Summary.htm') + shutil.copy(summary_source, summary_dest) + + body = get_unaligned_sample_export(lane, index_seq) + for split in ['001','002']: + for read in UNALIGNED_READS: + suffix = 'R{0}_{1}_export.txt.gz'.format(read, split) + pathname = paths.make_test_filename(suffix) + stream = gzip.open(pathname, 'w') + stream.write(body) + stream.close() + + +def make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id): + """Create a default mix of unaligned sample files + """ + for lane, read, name, index_id, index in UNALIGNED_SAMPLES: + make_unaligned_fastq_sample_1_12(unaligned_dir, + flowcell_id, + lane, + read, + name, + index_id, + index) + +def make_unaligned_fastq_sample_1_12(unaligned_dir, + flowcell_id, + lane, + reads, + project_id, + index_id=None, + index_seq=None): + + paths = DemultiplexedPaths(unaligned_dir, + flowcell_id, + lane, + project_id, + index_id, + index_seq) + paths.make_sample_dirs() + + sample_seq = get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq) + for split in ['001','002']: + for read in reads: + suffix = 'R{0}_{1}.fastq.gz'.format(read, split) + pathname = paths.make_test_filename(suffix) + stream = gzip.open(pathname, 'w') + stream.write(sample_seq) + stream.close() + + sheetname = os.path.join(paths.sample_dir, 'SampleSheet.csv') + stream = open(sheetname, 'w') + stream.write('FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject'+os.linesep) + template = '{flowcell},{lane},{id},mm9,{index},Sample #{id},N,PR_indexing,Operator,{sample_project}'+os.linesep + stream.write(template.format(flowcell=flowcell_id, + lane=lane, + id=paths.sample_id, + index=paths.index_seq, + sample_project=paths.sample_project)) + stream.close() + + +class DemultiplexedPaths(object): + def __init__(self, basedir, flowcell_id, lane, project_id, index_id, index_seq): + if lane not in LANE_LIST: + raise ValueError("Invalid lane ID: {0}".format(lane)) + self.basedir = basedir + self.flowcell_id = flowcell_id + self.lane = lane + + if project_id is None: + # undetermined + self.index_seq = '' + self.sample_id = 'lane{0}'.format(lane) + self.sample_project = 'Undetermined_indices' + self.rootname = 'lane{lane}_Undetermined_L00{lane}_'.format( + lane=lane) + self.project_dir = 'Undetermined_indices' + self.sample_dir = 'Sample_lane{lane}'.format(lane=lane) + elif index_seq is None: + self.index_seq = '' + self.sample_id = project_id + self.sample_project = '{project_id}'.format(project_id=project_id) + self.rootname = '{project_id}_NoIndex_L00{lane}_'.format( + project_id=project_id, + lane=lane) + self.project_dir = 'Project_' + self.sample_project + self.sample_dir = 'Sample_{project_id}'.format( + project_id=project_id) + else: + self.index_seq = index_seq + self.sample_id = project_id + self.sample_project = '{project_id}_Index{index_id}'.format( + project_id=project_id, + index_id=index_id) + self.rootname = '{project_id}_{index}_L00{lane}_'.format( + project_id=project_id, + index=index_seq, + lane=lane) + self.project_dir = 'Project_' + self.sample_project + self.sample_dir = 'Sample_{project_id}'.format( + project_id=project_id) + + self.project_dir = os.path.join(self.basedir, self.project_dir) + self.sample_dir = os.path.join(self.project_dir, self.sample_dir) + self.summary_dir = 'Summary_Stats_{0}'.format(self.flowcell_id) + self.summary_dir = os.path.join(self.project_dir, self.summary_dir) + print "HI:", self.summary_dir + + + def make_sample_dirs(self): + if not os.path.isdir(self.project_dir): + os.mkdir(self.project_dir) + if not os.path.isdir(self.sample_dir): + os.mkdir(self.sample_dir) + + def make_summary_dirs(self): + print "HI:", self.summary_dir + if not os.path.isdir(self.summary_dir): + os.mkdir(self.summary_dir) + + def make_test_filename(self, suffix): + filename = self.rootname + suffix + pathname = os.path.join(self.sample_dir, filename) + return pathname + def dump(self): + print ('index seq: {0}'.format(self.index_seq)) + + print ('project dir: {0}'.format(self.project_dir)) + print ('sample dir: {0}'.format(self.sample_dir)) + print ('rootname: {0}'.format(self.rootname)) + print ('path: {0}'.format( + os.path.join(self.project_dir, + self.sample_dir, + self.rootname+'R1_001.fastq.gz'))) + + +def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq): + seq = """@HWI-ST0787:101:{flowcell}:{lane}:1101:2416:3469 1:Y:0:{index} +TCCTTCATTCCACCGGAGTCTGTGGAATTCTCGGGTGCCAAGGAACTCCA ++ +CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJIIJJIIJJJJJ +@HWI-ST0787:101:{flowcell}:{lane}:1101:2677:3293 1:Y:0:{index} +TGGAAATCCATTGGGGTTTCCCCTGGAATTCTCGGGTGCCAAGGAACTCC ++ +@CCFF3BDHHHHHIIIIIHHIIIDIIIGIIIEGIIIIIIIIIIIIIIIHH +@HWI-ST0787:101:{flowcell}:{lane}:1101:2616:3297 1:Y:0:{index} +TAATACTGCCGGGTAATGATGGCTGGAATTCTCGGGTGCCAAGGAACTCC ++ +CCCFFFFFHHHHHCGHJJJJJJJJJJJJJJJJJIIJJJJJJJJJIHJJJI +@HWI-ST0787:101:{flowcell}:{lane}:1101:2545:3319 1:N:0:{index} +TCCTTCATTCCACCGGAGTCTGCTGGAATTCTCGGGTGCCAAGGAACTCC ++ +CCCFFFFFHHHFHJGIGHIJHIIGHIGIGIGEHFIJJJIHIJHJIIJJIH +""".format(flowcell=flowcell_id, lane=lane, index=index_seq) + return seq + +def get_unaligned_sample_export(lane, index_seq): + body = """HWI-ST0787\t102\t{lane}\t1101\t1207\t1993\t{index}\t1\tAANGGATTCGATCCGGCTTAAGAGATGAAAACCGAAAGGGCCGACCGAA\taaBS`ccceg[`ae[dRR_[[SPPPP__ececfYYWaegh^\\ZLLY\\X`\tNM\t\t\t\t\t\t +HWI-ST0787\t102 {lane} 1101 1478 1997 {index} 1 CAAGAACCCCGGGGGGGGGGGGGCAGAGAGGGGGAATTTTTTTTTTGTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NM N +HWI-ST0787 102 {lane} 1101 1625 1994 {index} 1 AANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA \^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c chrII.fa +""".format(lane=lane, index=index_seq) + return body def ls_tree(root): for dirpath, dirnames, filenames in os.walk(root): diff --git a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py new file mode 100644 index 0000000..927cf61 --- /dev/null +++ b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py @@ -0,0 +1,291 @@ +#!/usr/bin/env python + +from datetime import datetime, date +import os +import tempfile +import shutil +import unittest + +from htsworkflow.pipelines import eland +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 + flowcell_id = 'D07K6ACXX' + temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_') + + runfolder_dir = os.path.join(temp_dir, + '110815_SN787_0101_A{0}'.format(flowcell_id)) + os.mkdir(runfolder_dir) + + data_dir = os.path.join(runfolder_dir, 'Data') + os.mkdir(data_dir) + + intensities_dir = make_rta_intensities_1_12(data_dir) + + basecalls_dir = make_rta_basecalls_1_12(intensities_dir) + make_matrix_dir_rta_1_12(basecalls_dir) + + unaligned_dir = os.path.join(runfolder_dir, "Unaligned") + os.mkdir(unaligned_dir) + make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id) + make_unaligned_config_1_12(unaligned_dir) + + aligned_dir = os.path.join(runfolder_dir, "Aligned") + os.mkdir(aligned_dir) + make_aligned_eland_export(aligned_dir, flowcell_id) + make_aligned_config_1_12(aligned_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 = intensities_dir + obj.bustard_dir = unaligned_dir + obj.gerald_dir = aligned_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_bustard(self): + """Construct a bustard object""" + b = bustard.bustard(self.bustard_dir) + self.failUnlessEqual(b.version, '1.8.70.0') + self.failUnlessEqual(b.date, None) + self.failUnlessEqual(b.user, None) + self.failUnlessEqual(len(b.phasing), 0) + + 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) + + 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 1.171 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())) + + + # 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/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_extended') + self.failUnlessEqual(cur_lane.eland_genome, genomes[i]) + 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_extended') + self.failUnlessEqual(l.read_length, '37') + self.failUnlessEqual(l.use_bases, 'Y'*37) + + # test data extracted from summary file + clusters = [None, + (281331, 11169), (203841, 13513), + (220889, 15653), (137294, 14666), + (129388, 14525), (262092, 10751), + (185754, 13503), (233765, 9537),] + + self.failUnlessEqual(len(g.summary), 1) + for i in range(1,9): + summary_lane = g.summary[0][i] + self.failUnlessEqual(summary_lane.cluster, clusters[i]) + self.failUnlessEqual(summary_lane.lane, 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) + return + + # 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[i] + g2_lane = g2.lanes[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 + self.failUnlessEqual(len(g.summary), 1) + for i in range(1,9): + g_summary = g.summary[0][i] + g2_summary = g2.summary[0][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.results[0].keys(): + g_results = g_eland.results[0][lane] + g2_results = g2_eland.results[0][lane] + self.failUnlessEqual(g_results.reads, + g2_results.reads) + 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]) + + + def test_eland(self): + return + 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_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps) + + # 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(len(lane.mapped_reads), 17) + self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4) + 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['U2'], 0) + self.failUnlessEqual(lane.match_codes['R2'], 12) + self.failUnlessEqual(lane.match_codes['NM'], 1) + self.failUnlessEqual(lane.match_codes['QC'], 0) + + # 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_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) + 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): + return + runs = runfolder.get_runs(self.runfolder_dir) + + # do we get the flowcell id from the filename? + self.failUnlessEqual(len(runs), 1) + name = 'run_4286GAAXX_%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") + class Test(object): pass + t = Test() + make_runfolder(t) + print ('path ' + t.runfolder_dir) + diff --git a/htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml b/htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml new file mode 100644 index 0000000..2b7f3af --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml @@ -0,0 +1,234 @@ + + + + + + none + fileName + on + + + off + 3 + + *.fa + + + + + + + *.fa + off + 32 + + domain.com + ${logName} + localhost:25 + /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM + Flat.txt.gz + D07K6ACXX + _gene.md.gz + + --muf 0 + --mmaq 4 + 2 + .oa + 1 + 50 + 2 + /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM + + + 1 + 49 + $(WC) -l + totalClusters + ($(GREP) -cvE '^((NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$|splice_sites)' || exit 0) + genomeUsable + ($(FGREP) -wc NM || exit 0) + noMatch + $(WC) -l + PFClusters + ($(FGREP) -wc QC || exit 0) + QC + ($(FGREP) -wc RM || exit 0) + repeatMasked + ($(FGREP) -c splice_sites || exit 0) + spliceUsable + $(CUT) -f13 |($(EGREP) [0-9] || exit 0)|$(WC) -l + usable + ($(GREP) -vE '^(NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$' || exit 0) + + + + -v $(CASAVA_LOG_LEVEL) + + + y*n + yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn + http://host.domain.com/yourshare/ + true + + + + + + eland_extended + fileName + /mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/ + *.fa + 32 + 1 + 49 + 1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 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a/htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml b/htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml new file mode 100755 index 0000000..6d43157 --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml @@ -0,0 +1,472 @@ + + + + + + 0 + 0 + 0 + 0 + 0 + + + 0 + 0 + 0 + 0 + 0 + + 1 + 50 + 110815_SN787_0101_AD07K6ACXX + + + 51 + 57 + 110815_SN787_0101_AD07K6ACXX + + HWI-ST0787 + 0 + 0 + 0 + 0 + + 1 + 50 + 110815_SN787_0101_AD07K6ACXX + + + 51 + 57 + 110815_SN787_0101_AD07K6ACXX + + 110815_SN787_0101_AD07K6ACXX + 110815 + 0101 + D07K6ACXX + + 51 + 52 + 53 + 54 + 55 + 56 + 57 + + New6 + + + + + s + 1101 + 1102 + 1104 + 1103 + 1106 + 1105 + 1108 + 1107 + 1201 + 1204 + 1202 + 1205 + 1206 + 1208 + 1301 + 1302 + 1304 + 1203 + 1305 + 1306 + 1308 + 2102 + 2101 + 1207 + 2105 + 2106 + 2104 + 1303 + 2201 + 2202 + 1307 + 2206 + 2205 + 2108 + 2302 + 2103 + 2301 + 2204 + 2305 + 2107 + 2203 + 2208 + 2306 + 2207 + 2304 + 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Sample Summary Information For Experiment (12564_index6)

+

Project Summary

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Project Name12564_index6
MachineHWI-ST0787
Run Folder111221_SN787_0107_AD0CV5ACXX
Flow Cell IDD0CV5ACXX
Platform
Control SoftwareHiSeq Control Software 1.4.8
Primary AnalysisRTA 1.12.4.2
Secondary AnalysisCASAVA-1.8.1
+

Project Results Summary

+ + + + + + + + + + + +
Clusters (Raw)Clusters(PF)Yield (MBases)
658,174475,61823
+

Barcode-Lane summary

+
++++++++++ + + + + + + + + + + +
Barcode-LaneSampleBarcodeLaneSpeciesAnalysis TypeLengthNum TilesGenome Directory
+
++++++++++ + + + + + + + + + + +
12564_GCCAAT_L512564GCCAAT5Homo_sapienseland extended49 48/mmjggl/nicodemus/data01/genomes/hg18/chromosomes//*.fa
+

Sample Results Summary : Read 1

+
+++++++++++++ + + + + + + + + + + + + + + +
Sample Info
SampleSample Yield (Mbases)Clusters (raw)Clusters (PF)1st Cycle Int (PF)% intensity after 20 cycles (PF)% PF Clusters% Align (PF)Alignment Score (PF)% Mismatch Rate (PF)% >=Q30 bases (PF)Mean Quality SCore (PF)
+
+++++++++++++ + + + + + + + + + + + + + +
1256423658,174475,618110089.3972.2676.89128.730.4088.7935.13
+

Sample Results Summary : Read 2

+
+++++++++++++ + + + + + + + + + + + + + + +
Sample Info
SampleSample Yield (Mbases)Clusters (raw)Clusters (PF)1st Cycle Int (PF)% intensity after 20 cycles (PF)% PF Clusters% Align (PF)Alignment Score (PF)% Mismatch Rate (PF)% >=Q30 bases (PF)Mean Quality SCore (PF)
+
+++++++++++++ + + + + + + + + + + + + + +
1256400000
+

Expanded Sample Summary : Read 1

+
++++++++++++++ + + + + + + + + + + + + + + + + + + + + +
Sample InfoPhasing InfoRaw dataFiltered data
SampleClusters (raw)% Phasing% Prephasing% Mismatch Rate (raw)% PF ClustersCycle 2-4 Av Int (PF)Cycle 2-10 Av % Loss (PF)Cycle 10-20 Av % Loss (PF)% Align (PF)% Mismatch Rate (PF)% >=Q30 bases (PF)Mean Quality SCore (PF)
+
++++++++++++++ + + + + + + + + + + + + + + +
12564658,1740.190.310.7772.261083.00-84.760.4876.890.4088.7935.13
+

Expanded Sample Summary : Read 2

+
++++++++++++++ + + + + + + + + + + + + + + + + + + + + +
Sample InfoPhasing InfoRaw dataFiltered data
SampleClusters (raw)% Phasing% Prephasing% Mismatch Rate (raw)% PF ClustersCycle 2-4 Av Int (PF)Cycle 2-10 Av % Loss (PF)Cycle 10-20 Av % Loss (PF)% Align (PF)% Mismatch Rate (PF)% >=Q30 bases (PF)Mean Quality SCore (PF)
+
++++++++++++++ + + + + + + + + + + + + + + +
12564000000
+

IVC Plots

+ +click here +

All Intensity Plots

+ +click here +

Mismatch Graphs

+ +click here +

Mismatch Curves

+ +click here +

Additional Paired Statistics

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Sample InfoRelative Orientation StatisticsInsert Size Statistics (for relative orientation R+)Insert Statistics (% of individually uniquely alignable pairs)
SampleF-:
>R2 R1>		F+:
>R1 R2>		R-:
<R2 R1>		R+:
>R1 R2<		TotalMedianBelow-median SDAbove-median SDLow thresh.High thresh.Too smallToo largeOrientation and size OK
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125640
+

CASAVA-1.8.1

+ + -- 2.30.2