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Merge pull request #465 from ces/pacbio26
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PacBio IsoSeq analysis loading changes
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@jmtcsngr
jmtcsngr authored Aug 7, 2024
2 parents 374433d + 1d1d68a commit 2b5eb0c
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Unreleased

- SMRT Link IsoSeq analysis has changed substantially in SMRT Link v13
so old code and tests related to this was removed - further work is
planned in this area to remove the Sequel subdirectory entirely. As
it is an evolving area in sporadic use the loading code for IsoSeq
analysis was moved to a separate new IsoSeqPublisher module.
- added new WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher module
which handles loading of analysis output from SMRT Link
pb_segment_reads_and_isoseq jobs
- old code for IsoSeq loading completely removed from
WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher

Release 2.49.2
- Prevent access to a live mlwh database from tests.

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147 changes: 100 additions & 47 deletions MANIFEST
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Expand Up @@ -57,18 +57,20 @@ lib/WTSI/NPG/HTS/Illumina/RunPublisher.pm
lib/WTSI/NPG/HTS/Illumina/XMLDataObject.pm
lib/WTSI/NPG/HTS/LIMSFactory.pm
lib/WTSI/NPG/HTS/Metadata.pm
lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm
lib/WTSI/NPG/HTS/PacBio/Annotator.pm
lib/WTSI/NPG/HTS/PacBio/DataObjectFactory.pm
lib/WTSI/NPG/HTS/PacBio/Metadata.pm
lib/WTSI/NPG/HTS/PacBio/MetaQuery.pm
lib/WTSI/NPG/HTS/PacBio/MetaUpdater.pm
lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm
lib/WTSI/NPG/HTS/PacBio/RunPublisher.pm
lib/WTSI/NPG/HTS/PacBio/PublisherBase.pm
lib/WTSI/NPG/HTS/PacBio/SeqDataObject.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReport.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchive.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisher.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/MetaXMLParser.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/MonitorBase.pm
lib/WTSI/NPG/HTS/PacBio/Sequel/Product.pm
Expand Down Expand Up @@ -16638,48 +16640,6 @@ t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/
t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/m64089e_210503_164858.hifi_reads.bam.bai
t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/m64089e_210503_164858.hifi_reads.bam.pbi
t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/merged_analysis_report.json
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/hq_transcripts-1.fasta
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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/hq_transcripts-3.fasta
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/hq_transcripts-4.fasta
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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/hq_transcripts-6.fasta
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/hq_transcripts-7.fasta
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/hq_transcripts-8.fasta
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/lq_transcripts-1.fasta
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-demux_cluster_files/execution/lq_transcripts-2.fasta
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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1001_5p--bc1001_3p.bam
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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1001_5p--bc1001_3p.consensusreadset.xml
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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1002_5p--bc1002_3p.bam.pbi
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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1003_5p--bc1003_3p.bam
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1003_5p--bc1003_3p.bam.pbi
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1003_5p--bc1003_3p.consensusreadset.xml
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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1004_5p--bc1004_3p.bam.pbi
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1004_5p--bc1004_3p.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1005_5p--bc1005_3p.bam
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1005_5p--bc1005_3p.bam.pbi
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1005_5p--bc1005_3p.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1006_5p--bc1006_3p.bam
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1006_5p--bc1006_3p.bam.pbi
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1006_5p--bc1006_3p.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1008_5p--bc1008_3p.bam
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1008_5p--bc1008_3p.bam.pbi
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1008_5p--bc1008_3p.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1012_5p--bc1012_3p.bam
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1012_5p--bc1012_3p.bam.pbi
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1012_5p--bc1012_3p.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/merged_analysis_report.json
t/data/pacbio/sequel_analysis/0000004117/entry-points/222a1be3-85b1-12b3-b3bc-9742f8e22f95.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/lima_guesses.report.json
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json
Expand Down Expand Up @@ -16716,6 +16676,101 @@ t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execu
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-1.fasta
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-1.gff
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-2.fasta
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-2.gff
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-3.fasta
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t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-4.fasta
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t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-5.fasta
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms-5.gff
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-1.txt
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-2.txt
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-3.txt
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-4.txt
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-5.txt
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.group-1.txt
t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.group-2.txt
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t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.read_stat-1.txt
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t/data/pacbio/sequel_analysis/0000020083/outputs/collapse_isoforms.read_stat-5.txt
t/data/pacbio/sequel_analysis/0000020083/outputs/flnc-1.bam
t/data/pacbio/sequel_analysis/0000020083/outputs/flnc-2.bam
t/data/pacbio/sequel_analysis/0000020083/outputs/flnc-3.bam
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t/data/pacbio/sequel_analysis/0000020083/outputs/flnc.report-1.csv
t/data/pacbio/sequel_analysis/0000020083/outputs/flnc.report-2.csv
t/data/pacbio/sequel_analysis/0000020083/outputs/flnc.report-3.csv
t/data/pacbio/sequel_analysis/0000020083/outputs/flnc.report-4.csv
t/data/pacbio/sequel_analysis/0000020083/outputs/flnc.report-5.csv
t/data/pacbio/sequel_analysis/0000020083/outputs/isoseq_mapping.report.json
t/data/pacbio/sequel_analysis/0000020083/outputs/isoseq_primers.report.json
t/data/pacbio/sequel_analysis/0000020083/outputs/isoseq.report.json
t/data/pacbio/sequel_analysis/0000020083/outputs/mapped-1.bam
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t/data/pacbio/sequel_analysis/0000020083/outputs/mapped.bam-1.bai
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t/data/pacbio/sequel_analysis/0000020083/outputs/mapped.bam-5.bai
t/data/pacbio/sequel_analysis/0000020083/outputs/read_segmentation.report.json
t/data/pacbio/sequel_analysis/0000020083/outputs/sample0.transcripts.cluster_report.csv
t/data/pacbio/sequel_analysis/0000020083/outputs/sample0.transcripts.fl_counts.csv
t/data/pacbio/sequel_analysis/0000020083/outputs/sample1.transcripts.cluster_report.csv
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t/data/pacbio/sequel_analysis/0000020083/outputs/segmented.bam
t/data/pacbio/sequel_analysis/0000020083/outputs/segmented.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000020083/outputs/segmented.non_passing.bam
t/data/pacbio/sequel_analysis/0000020083/outputs/transcripts-1.fasta
t/data/pacbio/sequel_analysis/0000020083/outputs/transcripts-2.fasta
t/data/pacbio/sequel_analysis/0000020083/outputs/transcripts-3.fasta
t/data/pacbio/sequel_analysis/0000020083/outputs/transcripts-4.fasta
t/data/pacbio/sequel_analysis/0000020083/outputs/transcripts-5.fasta
t/data/pacbio/sequel_analysis/0000020156/outputs/collapse_isoforms.fasta
t/data/pacbio/sequel_analysis/0000020156/outputs/collapse_isoforms.fl_count.txt
t/data/pacbio/sequel_analysis/0000020156/outputs/collapse_isoforms.flnc_count.txt
t/data/pacbio/sequel_analysis/0000020156/outputs/collapse_isoforms.gff
t/data/pacbio/sequel_analysis/0000020156/outputs/collapse_isoforms.group.txt
t/data/pacbio/sequel_analysis/0000020156/outputs/collapse_isoforms.read_stat.txt
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc-1.bam
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc-2.bam
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t/data/pacbio/sequel_analysis/0000020156/outputs/flnc-4.bam
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc-5.bam
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc.report-1.csv
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc.report-2.csv
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc.report-3.csv
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc.report-4.csv
t/data/pacbio/sequel_analysis/0000020156/outputs/flnc.report-5.csv
t/data/pacbio/sequel_analysis/0000020156/outputs/isoseq_mapping.report.json
t/data/pacbio/sequel_analysis/0000020156/outputs/isoseq_primers.report.json
t/data/pacbio/sequel_analysis/0000020156/outputs/isoseq.report.json
t/data/pacbio/sequel_analysis/0000020156/outputs/mapped.bam
t/data/pacbio/sequel_analysis/0000020156/outputs/mapped.bam.bai
t/data/pacbio/sequel_analysis/0000020156/outputs/read_segmentation.report.json
t/data/pacbio/sequel_analysis/0000020156/outputs/sample0.transcripts.cluster_report.csv
t/data/pacbio/sequel_analysis/0000020156/outputs/sample0.transcripts.fl_counts.csv
t/data/pacbio/sequel_analysis/0000020156/outputs/segmented.bam
t/data/pacbio/sequel_analysis/0000020156/outputs/segmented.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000020156/outputs/segmented.non_passing.bam
t/data/pacbio/sequel_analysis/0000020156/outputs/transcripts.fasta
t/data/pacbio_meta_updater/m131209_183112_00127_c100579142550000001823092301191430_s1_p0.1.bax.h5
t/data/pacbio_seq_data_object/m54097_161031_165824.subreads.bam
t/data/pacbio_seq_data_object/m54097_161207_133626.subreads.bam
Expand Down Expand Up @@ -16783,13 +16838,12 @@ t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm
t/lib/WTSI/NPG/HTS/Illumina/RunPublisherTest.pm
t/lib/WTSI/NPG/HTS/LIMSFactoryTest.pm
t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm
t/lib/WTSI/NPG/HTS/PacBio/RunPublisherTest.pm
t/lib/WTSI/NPG/HTS/PacBio/SeqDataObjectTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisFastaManagerTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReportTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchiveTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisherTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditorTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitorTest.pm
t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteTest.pm
Expand All @@ -16806,13 +16860,12 @@ t/lib/WTSI/NPG/OM/BioNano/Saphyr/RunPublisherTest.pm
t/log_publisher.t
t/location_writer.t
t/pacbio_meta_updater.t
t/pacbio_run_publisher.t
t/pacbio_seq_data_object.t
t/pacbio_sequel_analysis_fasta_manager.t
t/pacbio_sequel_analysis_monitor.t
t/pacbio_sequel_analysis_publisher.t
t/pacbio_sequel_analysis_report.t
t/pacbio_sequel_image_archive.t
t/pacbio_sequel_isoseq_publisher.t
t/pacbio_sequel_run_auditor.t
t/pacbio_sequel_run_delete_monitor.t
t/pacbio_sequel_run_delete.t
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