Index

_

_add_mapped_reads_column() (bripipetools.postprocessing.stitching.OutputStitcher method) _append_processed_data() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method) _assign_workflow() (bripipetools.submission.samplesubmit.SampleSubmissionBuilder method) _assign_workflows() (bripipetools.submission.flowcellsubmit.FlowcellSubmissionBuilder method) _build_batch_name() (bripipetools.submission.batchcreate.BatchCreator method) _build_combined_filename() (bripipetools.postprocessing.compiling.OutputCompiler method) (bripipetools.postprocessing.stitching.OutputStitcher method) _build_output_path() (bripipetools.submission.batchparameterize.BatchParameterizer method) _build_overrepresented_seq_table() (bripipetools.postprocessing.stitching.OutputStitcher method) _build_reference_path() (bripipetools.submission.batchparameterize.BatchParameterizer method) _build_sample_parameters() (bripipetools.submission.batchparameterize.BatchParameterizer method) _build_table() (bripipetools.postprocessing.compiling.OutputCompiler method) (bripipetools.postprocessing.stitching.OutputStitcher method) _check_input_type() (bripipetools.submission.batchcreate.BatchCreator method) _check_sex() (bripipetools.annotation.workflowbatches.WorkflowBatchAnnotator method) _check_table_format() (bripipetools.io.picardmetrics.PicardMetricsFile method) _clean_header() (bripipetools.io.fastqc.FastQCFile method) _clean_output_paths() (bripipetools.monitoring.workflowbatches.WorkflowBatchMonitor method) _clean_value() (bripipetools.io.fastqc.FastQCFile method) _collect_flowcellrun() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _collect_librarygenecounts() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _collect_librarymetrics() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _collect_processedlibraries() (bripipetools.dbification.workflowbatch.WorkflowBatchImporter method) _collect_sequencedlibraries() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _collect_workflowbatch() (bripipetools.dbification.workflowbatch.WorkflowBatchImporter method) _compute_x_y_data() (bripipetools.qc.sexcheck.SexChecker method) _compute_y_x_count_ratio() (bripipetools.qc.sexpredict.SexPredictor method) _compute_y_x_gene_ratio() (bripipetools.qc.sexpredict.SexPredictor method) _flowcell_path (bripipetools.model.documents.FlowcellRun attribute) _get_batch_tags() (bripipetools.submission.flowcellsubmit.FlowcellSubmissionBuilder method) _get_counts_path() (bripipetools.qc.sexcheck.SexChecker method) _get_input_params() (bripipetools.submission.batchcreate.BatchCreator method) _get_lane_fastq() (bripipetools.submission.batchparameterize.BatchParameterizer method) _get_lane_order() (bripipetools.submission.batchparameterize.BatchParameterizer method) _get_output_paths() (bripipetools.postprocessing.cleanup.OutputCleaner method) _get_output_types() (bripipetools.postprocessing.cleanup.OutputCleaner method) _get_outputs() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method) (bripipetools.monitoring.workflowbatches.WorkflowBatchMonitor method) (bripipetools.postprocessing.stitching.OutputStitcher method) _get_parser() (bripipetools.postprocessing.stitching.OutputStitcher method) _get_project_paths() (bripipetools.submission.flowcellsubmit.FlowcellSubmissionBuilder method) _get_raw_data() (bripipetools.annotation.sequencedlibs.SequencedLibraryAnnotator method) _get_sample_paths() (bripipetools.submission.batchcreate.BatchCreator method) _get_section_status() (bripipetools.io.fastqc.FastQCFile method) _get_seqlib_id() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method) _get_table() (bripipetools.io.picardmetrics.PicardMetricsFile method) _get_x_y_counts() (bripipetools.qc.sexcheck.SexChecker method) _group_outputs() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method) _init_annotator() (bripipetools.submission.flowcellsubmit.FlowcellSubmissionBuilder method) _init_flowcellrun() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) _init_importer() (bripipetools.dbification.control.ImportManager method) _init_processedlibrary() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method)

_init_sequencedlibrary() (bripipetools.annotation.sequencedlibs.SequencedLibraryAnnotator method) _init_workflowbatch() (bripipetools.annotation.workflowbatches.WorkflowBatchAnnotator method) _insert_genomicsFlowcellRun() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _insert_genomicsLibrarymetrics() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _insert_genomicsProcessedlibraries() (bripipetools.dbification.workflowbatch.WorkflowBatchImporter method) _insert_genomicsSequencedlibraries() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _insert_genomicsWorkflowbatch() (bripipetools.dbification.workflowbatch.WorkflowBatchImporter method) _insert_genomicsWorkflowbatches() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _insert_librarygenecounts() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) _load_x_genes() (bripipetools.qc.sexcheck.SexChecker method) _load_y_genes() (bripipetools.qc.sexcheck.SexChecker method) _locate_batch_name_line() (bripipetools.io.workflowbatch.WorkflowBatchFile method) _locate_param_line() (bripipetools.io.workflowbatch.WorkflowBatchFile method) _locate_sample_start_line() (bripipetools.io.workflowbatch.WorkflowBatchFile method) _locate_sections() (bripipetools.io.fastqc.FastQCFile method) _locate_workflow_name_line() (bripipetools.io.workflowbatch.WorkflowBatchFile method) _parse_lines() (bripipetools.io.htseqmetrics.HtseqMetricsFile method) (bripipetools.io.sexcheck.SexcheckFile method) (bripipetools.io.tophatstats.TophatStatsFile method) _parse_long() (bripipetools.io.picardmetrics.PicardMetricsFile method) _parse_output_name() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method) _parse_section_table() (bripipetools.io.fastqc.FastQCFile method) _parse_wide() (bripipetools.io.picardmetrics.PicardMetricsFile method) _predict_sex() (bripipetools.qc.sexcheck.SexChecker method) (bripipetools.qc.sexpredict.SexPredictor method) _prep_output_dir() (bripipetools.submission.batchparameterize.BatchParameterizer method) _prep_target_dir() (bripipetools.submission.batchcreate.BatchCreator method) _read_data() (bripipetools.postprocessing.compiling.OutputCompiler method) (bripipetools.postprocessing.stitching.OutputStitcher method) _read_file() (bripipetools.io.fastqc.FastQCFile method) (bripipetools.io.htseqcounts.HtseqCountsFile method) (bripipetools.io.htseqmetrics.HtseqMetricsFile method) (bripipetools.io.picardmetrics.PicardMetricsFile method) (bripipetools.io.sexcheck.SexcheckFile method) (bripipetools.io.tophatstats.TophatStatsFile method) (bripipetools.io.workflow.WorkflowFile method) (bripipetools.io.workflowbatch.WorkflowBatchFile method) _read_paths() (bripipetools.submission.samplesubmit.SampleSubmissionBuilder method) _recode_output() (bripipetools.postprocessing.cleanup.OutputCleaner method) _retrieve_sex() (bripipetools.qc.sexverify.SexVerifier method) _run_qc() (bripipetools.annotation.workflowbatches.WorkflowBatchAnnotator method) _set_option_value() (bripipetools.submission.batchparameterize.BatchParameterizer method) _sniff_output_type() (bripipetools.postprocessing.stitching.OutputStitcher method) _sniff_path() (bripipetools.dbification.control.ImportManager method) _unnest_output() (bripipetools.postprocessing.cleanup.OutputCleaner method) _unzip_output() (bripipetools.postprocessing.cleanup.OutputCleaner method) _update_flowcellrun() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) _update_processedlibrary() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method) _update_sequencedlibrary() (bripipetools.annotation.sequencedlibs.SequencedLibraryAnnotator method) _update_workflowbatch() (bripipetools.annotation.workflowbatches.WorkflowBatchAnnotator method) _verify_sex() (bripipetools.qc.sexcheck.SexChecker method) _write_data() (bripipetools.qc.sexcheck.SexChecker method)

B

BatchCreator (class in bripipetools.submission.batchcreate) BatchParameterizer (class in bripipetools.submission.batchparameterize) bripipetools.annotation (module) bripipetools.annotation.flowcellruns (module) bripipetools.annotation.processedlibs (module) bripipetools.annotation.sequencedlibs (module) bripipetools.annotation.workflowbatches (module) bripipetools.database (module) bripipetools.database.connection (module) bripipetools.database.mapping (module) bripipetools.database.operations (module) bripipetools.dbification (module) bripipetools.dbification.control (module) bripipetools.dbification.flowcellrun (module) bripipetools.dbification.workflowbatch (module) bripipetools.io (module) bripipetools.io.fastqc (module) bripipetools.io.htseqcounts (module) bripipetools.io.htseqmetrics (module) bripipetools.io.picardmetrics (module) bripipetools.io.sexcheck (module) bripipetools.io.tophatstats (module) bripipetools.io.workflow (module) bripipetools.io.workflowbatch (module)

bripipetools.model (module) bripipetools.model.documents (module) bripipetools.monitoring (module) bripipetools.monitoring.workflowbatches (module) bripipetools.parsing (module) bripipetools.parsing.gencore (module) bripipetools.parsing.illumina (module) bripipetools.parsing.processing (module) bripipetools.postprocessing (module) bripipetools.postprocessing.cleanup (module) bripipetools.postprocessing.compiling (module) bripipetools.postprocessing.stitching (module) bripipetools.qc (module) bripipetools.qc.sexcheck (module) bripipetools.qc.sexpredict (module) bripipetools.qc.sexverify (module) bripipetools.submission (module) bripipetools.submission.batchcreate (module) bripipetools.submission.batchparameterize (module) bripipetools.submission.flowcellsubmit (module) bripipetools.submission.samplesubmit (module) bripipetools.util (module) bripipetools.util.files (module) bripipetools.util.strings (module)

C

check_outputs() (bripipetools.monitoring.workflowbatches.WorkflowBatchMonitor method) check_project_outputs() (bripipetools.monitoring.workflowbatches.WorkflowBatchMonitor method) clean_outputs() (bripipetools.postprocessing.cleanup.OutputCleaner method)

connect() (in module bripipetools.database.connection) convert_keys() (in module bripipetools.model.documents) create_batch() (bripipetools.submission.batchcreate.BatchCreator method) create_workflowbatch_id() (in module bripipetools.database.operations)

F

FastQCFile (class in bripipetools.io.fastqc) find_objects() (in module bripipetools.database.operations) flowcell_path() (bripipetools.model.documents.FlowcellRun property)

FlowcellRun (class in bripipetools.model.documents) FlowcellRunAnnotator (class in bripipetools.annotation.flowcellruns) FlowcellRunImporter (class in bripipetools.dbification.flowcellrun) FlowcellSubmissionBuilder (class in bripipetools.submission.flowcellsubmit)

G

GalaxyWorkflowBatch (class in bripipetools.model.documents) gene_counts() (bripipetools.model.documents.GeneCounts property) GeneCounts (class in bripipetools.model.documents) GenericRun (class in bripipetools.model.documents) GenericSample (class in bripipetools.model.documents) GenericWorkflow (class in bripipetools.model.documents) GenericWorkflowBatch (class in bripipetools.model.documents) get_batch_name() (bripipetools.io.workflowbatch.WorkflowBatchFile method) get_flowcell_id() (in module bripipetools.parsing.illumina) get_flowcell_path() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) get_flowcell_run() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) get_genomicsCounts() (in module bripipetools.database.operations) get_genomicsMetrics() (in module bripipetools.database.operations) get_genomicsRuns() (in module bripipetools.database.operations) get_genomicsSamples() (in module bripipetools.database.operations) get_genomicsWorkflowbatches() (in module bripipetools.database.operations) get_libraries() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) get_library_gene_counts() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) get_library_id() (in module bripipetools.parsing.gencore) get_library_metrics() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method)

get_model_class() (in module bripipetools.database.mapping) get_params() (bripipetools.io.workflowbatch.WorkflowBatchFile method) get_processed_libraries() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) (bripipetools.annotation.workflowbatches.WorkflowBatchAnnotator method) get_processed_library() (bripipetools.annotation.processedlibs.ProcessedLibraryAnnotator method) get_processed_projects() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) get_project_label() (in module bripipetools.parsing.gencore) get_projects() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) get_sample_id() (in module bripipetools.parsing.gencore) get_sample_params() (bripipetools.io.workflowbatch.WorkflowBatchFile method) get_sequenced_libraries() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) (bripipetools.annotation.workflowbatches.WorkflowBatchAnnotator method) get_sequenced_library() (bripipetools.annotation.sequencedlibs.SequencedLibraryAnnotator method) get_tool_info() (bripipetools.io.workflow.WorkflowFile method) get_unaligned_path() (bripipetools.annotation.flowcellruns.FlowcellRunAnnotator method) get_workflow_batch() (bripipetools.annotation.workflowbatches.WorkflowBatchAnnotator method) get_workflow_name() (bripipetools.io.workflow.WorkflowFile method) (bripipetools.io.workflowbatch.WorkflowBatchFile method) get_workflow_options() (bripipetools.submission.flowcellsubmit.FlowcellSubmissionBuilder method) (bripipetools.submission.samplesubmit.SampleSubmissionBuilder method) GlobusGalaxyWorkflow (class in bripipetools.model.documents)

H

HtseqCountsFile (class in bripipetools.io.htseqcounts)

HtseqMetricsFile (class in bripipetools.io.htseqmetrics)

I

ImportManager (class in bripipetools.dbification.control) insert() (bripipetools.dbification.flowcellrun.FlowcellRunImporter method) (bripipetools.dbification.workflowbatch.WorkflowBatchImporter method)

insert_objects() (in module bripipetools.database.operations)

L

Library (class in bripipetools.model.documents)

locate_root_folder() (in module bripipetools.util.files)

M

map_keys() (in module bripipetools.database.mapping) map_to_object() (in module bripipetools.database.mapping) matchdefault() (in module bripipetools.util.strings)

matchlastdefault() (in module bripipetools.util.strings) Metrics (class in bripipetools.model.documents) metrics() (bripipetools.model.documents.Metrics property)

O

OutputCleaner (class in bripipetools.postprocessing.cleanup)

OutputCompiler (class in bripipetools.postprocessing.compiling) OutputStitcher (class in bripipetools.postprocessing.stitching)

P

parameterize() (bripipetools.submission.batchparameterize.BatchParameterizer method) parse() (bripipetools.io.fastqc.FastQCFile method) (bripipetools.io.htseqcounts.HtseqCountsFile method) (bripipetools.io.htseqmetrics.HtseqMetricsFile method) (bripipetools.io.picardmetrics.PicardMetricsFile method) (bripipetools.io.sexcheck.SexcheckFile method) (bripipetools.io.tophatstats.TophatStatsFile method) (bripipetools.io.workflow.WorkflowFile method) (bripipetools.io.workflowbatch.WorkflowBatchFile method) parse_batch_file_path() (in module bripipetools.parsing.gencore) parse_batch_name() (in module bripipetools.parsing.processing) parse_fastq_filename() (in module bripipetools.parsing.illumina) parse_flowcell_path() (in module bripipetools.parsing.gencore) parse_flowcell_run_id() (in module bripipetools.parsing.illumina) parse_output_filename() (in module bripipetools.parsing.processing)

parse_output_name() (in module bripipetools.parsing.processing) parse_overrepresented_seqs() (bripipetools.io.fastqc.FastQCFile method) parse_project_label() (in module bripipetools.parsing.gencore) parse_run_id_for_batch() (in module bripipetools.parsing.processing) parse_workflow_param() (in module bripipetools.parsing.processing) PicardMetricsFile (class in bripipetools.io.picardmetrics) predict() (bripipetools.qc.sexpredict.SexPredictor method) processed_data() (bripipetools.model.documents.ProcessedLibrary property) ProcessedLibrary (class in bripipetools.model.documents) ProcessedLibraryAnnotator (class in bripipetools.annotation.processedlibs) put_genomicsCounts() (in module bripipetools.database.operations) put_genomicsMetrics() (in module bripipetools.database.operations) put_genomicsRuns() (in module bripipetools.database.operations) put_genomicsSamples() (in module bripipetools.database.operations) put_genomicsWorkflowbatches() (in module bripipetools.database.operations)

R

raw_data() (bripipetools.model.documents.SequencedLibrary property) run() (bripipetools.dbification.control.ImportManager method) (bripipetools.submission.flowcellsubmit.FlowcellSubmissionBuilder method) (bripipetools.submission.samplesubmit.SampleSubmissionBuilder method)

S

SampleSubmissionBuilder (class in bripipetools.submission.samplesubmit) search_ancestors() (in module bripipetools.database.operations) SequencedLibrary (class in bripipetools.model.documents) SequencedLibraryAnnotator (class in bripipetools.annotation.sequencedlibs)

SexChecker (class in bripipetools.qc.sexcheck) SexcheckFile (class in bripipetools.io.sexcheck) SexPredictor (class in bripipetools.qc.sexpredict) SexVerifier (class in bripipetools.qc.sexverify) swap_root() (in module bripipetools.util.files)

T

TG3Object (class in bripipetools.model.documents) to_camel_case() (in module bripipetools.util.strings)

to_json() (bripipetools.model.documents.TG3Object method) to_snake_case() (in module bripipetools.util.strings) TophatStatsFile (class in bripipetools.io.tophatstats)

U

update() (bripipetools.qc.sexcheck.SexChecker method)

update_attrs() (bripipetools.model.documents.TG3Object method) update_batch_name() (bripipetools.io.workflowbatch.WorkflowBatchFile method)

V

verify() (bripipetools.qc.sexverify.SexVerifier method)

W

WorkflowBatchAnnotator (class in bripipetools.annotation.workflowbatches) WorkflowBatchFile (class in bripipetools.io.workflowbatch) WorkflowBatchImporter (class in bripipetools.dbification.workflowbatch) WorkflowBatchMonitor (class in bripipetools.monitoring.workflowbatches)

WorkflowFile (class in bripipetools.io.workflow) write() (bripipetools.io.workflowbatch.WorkflowBatchFile method) write_overrepresented_seq_table() (bripipetools.postprocessing.stitching.OutputStitcher method) write_table() (bripipetools.postprocessing.compiling.OutputCompiler method) (bripipetools.postprocessing.stitching.OutputStitcher method)