Index

A

add() (bcftbx.htmlpagewriter.HTMLPageWriter method) add_arg() (in module bcftbx.cmdparse) add_command() (bcftbx.cmdparse.CommandParser method) add_debug_option() (in module bcftbx.cmdparse) add_dir_to_zip() (in module bcftbx.qc.report) add_dry_run_option() (in module bcftbx.cmdparse) add_no_save_option() (in module bcftbx.cmdparse) add_nprocessors_option() (in module bcftbx.cmdparse) add_result() (bcftbx.Md5sum.Md5CheckReporter method) add_runner_option() (in module bcftbx.cmdparse) add_work_sheet() (bcftbx.simple_xls.XLSWorkBook method) addBoxplot() (bcftbx.qc.report.QCSample method) addCSSRule() (bcftbx.htmlpagewriter.HTMLPageWriter method) addDuplicateExperiment() (bcftbx.Experiment.ExperimentList method) addEmptyRow() (bcftbx.Spreadsheet.Spreadsheet method) addExperiment() (bcftbx.Experiment.ExperimentList method)

addFastQC() (bcftbx.qc.report.QCSample method) addJavaScript() (bcftbx.htmlpagewriter.HTMLPageWriter method) addProgramInfo() (bcftbx.qc.report.QCSample method) addRow() (bcftbx.Spreadsheet.Spreadsheet method) addSample() (bcftbx.qc.report.QCReporter method) addScreen() (bcftbx.qc.report.QCSample method) addSheet() (bcftbx.Spreadsheet.Workbook method) addTabData() (bcftbx.Spreadsheet.Worksheet method) addText() (bcftbx.Spreadsheet.Worksheet method) addTitleRow() (bcftbx.Spreadsheet.Spreadsheet method) append() (bcftbx.TabFile.TabDataLine method) (bcftbx.TabFile.TabFile method) append_column() (bcftbx.simple_xls.XLSWorkSheet method) append_row() (bcftbx.simple_xls.XLSWorkSheet method) appendColumn() (bcftbx.TabFile.TabDataLine method) (bcftbx.TabFile.TabFile method) AttributeDictionary (class in bcftbx.utils)

B

BaseJobRunner (class in bcftbx.JobRunner) bcftbx.cmdparse module bcftbx.Experiment module bcftbx.FASTQFile module bcftbx.htmlpagewriter module bcftbx.IlluminaData module bcftbx.JobRunner module bcftbx.Md5sum module bcftbx.ngsutils module

bcftbx.Pipeline module bcftbx.platforms module bcftbx.qc.report module bcftbx.simple_xls module bcftbx.SolidData module bcftbx.Spreadsheet module bcftbx.TabFile module bcftbx.utils module boxplots() (bcftbx.qc.report.QCSample method) buildAnalysisDirs() (bcftbx.Experiment.ExperimentList method)

C

CasavaSampleSheet (class in bcftbx.IlluminaData) cell() (in module bcftbx.simple_xls) CellIndex (class in bcftbx.simple_xls) chmod() (in module bcftbx.utils) chown() (bcftbx.utils.PathInfo method) cmp_column_indices() (in module bcftbx.simple_xls) column_id_from_index() (bcftbx.Spreadsheet.Worksheet method) column_index_to_integer() (in module bcftbx.simple_xls) column_integer_to_index() (in module bcftbx.simple_xls) column_is_empty() (bcftbx.simple_xls.XLSWorkSheet method) columnof() (bcftbx.simple_xls.XLSWorkSheet method)

ColumnRange (class in bcftbx.simple_xls) CommandParser (class in bcftbx.cmdparse) commonprefix() (in module bcftbx.utils) compute_md5sums() (bcftbx.Md5sum.Md5Checker class method) computeColumn() (bcftbx.TabFile.TabFile method) concatenate_fastq_files() (in module bcftbx.utils) convert_miseq_samplesheet_to_casava() (in module bcftbx.IlluminaData) convert_to_number() (in module bcftbx.simple_xls) convert_to_str() (bcftbx.TabFile.TabDataLine method) convert_to_type() (bcftbx.TabFile.TabDataLine method) convert_to_type_pep515() (bcftbx.TabFile.TabDataLine method) count_reads() (in module bcftbx.qc.report)

D

data_format (bcftbx.qc.report.QCReporter property) datetime (bcftbx.utils.PathInfo property) deepest_accessible_parent (bcftbx.utils.PathInfo property)

delimiter() (bcftbx.TabFile.TabDataLine method) describe_project() (in module bcftbx.IlluminaData) dirn (bcftbx.qc.report.QCReporter property)

E

encodePNG() (bcftbx.htmlpagewriter.PNGBase64Encoder method) errFile() (bcftbx.JobRunner.GEJobRunner method) (bcftbx.JobRunner.SimpleJobRunner method) (bcftbx.JobRunner.SlurmRunner method) error() (bcftbx.cmdparse.CommandParser method) errorState() (bcftbx.JobRunner.GEJobRunner method) (bcftbx.JobRunner.SimpleJobRunner method) (bcftbx.JobRunner.SlurmRunner method) eval_formula() (in module bcftbx.simple_xls)

excel_number_format (bcftbx.simple_xls.XLSStyle property) exists (bcftbx.utils.PathInfo property) Experiment (class in bcftbx.Experiment) ExperimentList (class in bcftbx.Experiment) extract_index() (in module bcftbx.utils) extract_index_as_string() (in module bcftbx.utils) extract_initials() (in module bcftbx.utils) extract_library_timestamp() (in module bcftbx.SolidData) extract_prefix() (in module bcftbx.utils)

F

FastqAttributes (class in bcftbx.FASTQFile) fastqc (bcftbx.qc.report.QCSample property) FastqIterator (class in bcftbx.FASTQFile) FastqRead (class in bcftbx.FASTQFile) fastqs_are_pair() (in module bcftbx.FASTQFile) fetch_runner() (in module bcftbx.JobRunner) filename() (bcftbx.TabFile.TabFile method) fill_column() (bcftbx.simple_xls.XLSWorkSheet method)

find_program() (in module bcftbx.utils) fix_bases_mask() (in module bcftbx.IlluminaData) format (bcftbx.FASTQFile.SequenceIdentifier property) format_file_size() (in module bcftbx.utils) format_value() (in module bcftbx.simple_xls) freezePanes() (bcftbx.Spreadsheet.Worksheet method) fsize (bcftbx.FASTQFile.FastqAttributes property) full_index() (bcftbx.simple_xls.XLSColumn method)

G

GEJobRunner (class in bcftbx.JobRunner) get_casava_sample_sheet() (in module bcftbx.IlluminaData) get_current_user() (in module bcftbx.utils) get_fastq_file_handle() (in module bcftbx.FASTQFile) get_gid_from_group() (in module bcftbx.utils) get_group_from_gid() (in module bcftbx.utils) get_primary_data_file_pair() (in module bcftbx.SolidData) get_run_completion_files() (in module bcftbx.platforms) get_sequencer_platform() (in module bcftbx.platforms) get_style() (bcftbx.simple_xls.XLSWorkSheet method) get_uid_from_user() (in module bcftbx.utils) get_unique_fastq_names() (in module bcftbx.IlluminaData) get_user_from_uid() (in module bcftbx.utils) getColumnId() (bcftbx.Spreadsheet.Worksheet method)

GetFastqFiles() (in module bcftbx.Pipeline) GetFastqGzFiles() (in module bcftbx.Pipeline) getLastExperiment() (bcftbx.Experiment.ExperimentList method) getlines() (in module bcftbx.utils) getPrimaryDataFiles() (bcftbx.qc.report.QCReporter method) getreads() (in module bcftbx.ngsutils) getreads_regex() (in module bcftbx.ngsutils) getreads_subset() (in module bcftbx.ngsutils) getSheet() (bcftbx.Spreadsheet.Workbook method) GetSolidDataFiles() (in module bcftbx.Pipeline) GetSolidPairedEndFiles() (in module bcftbx.Pipeline) getXfStyle() (bcftbx.Spreadsheet.Styles method) gid (bcftbx.utils.PathInfo property) group (bcftbx.utils.PathInfo property)

H

handle_generic_commands() (bcftbx.cmdparse.CommandParser method) header() (bcftbx.TabFile.TabFile method)

html (bcftbx.qc.report.QCReporter property) HTMLPageWriter (class in bcftbx.htmlpagewriter)

I

IEMSampleSheet (class in bcftbx.IlluminaData) IlluminaData (class in bcftbx.IlluminaData) IlluminaDataError (class in bcftbx.IlluminaData) IlluminaFastq (class in bcftbx.IlluminaData) IlluminaProject (class in bcftbx.IlluminaData) IlluminaQCReporter (class in bcftbx.qc.report) IlluminaQCSample (class in bcftbx.qc.report) IlluminaRun (class in bcftbx.IlluminaData) IlluminaRunInfo (class in bcftbx.IlluminaData) IlluminaSample (class in bcftbx.IlluminaData) incr_col() (in module bcftbx.simple_xls) indexByLineNumber() (bcftbx.TabFile.TabFile method) insert() (bcftbx.TabFile.TabFile method) insert_block_data() (bcftbx.simple_xls.XLSWorkSheet method) insert_column() (bcftbx.simple_xls.XLSWorkSheet method) insert_column_data() (bcftbx.simple_xls.XLSWorkSheet method) insert_row() (bcftbx.simple_xls.XLSWorkSheet method) insert_row_data() (bcftbx.simple_xls.XLSWorkSheet method) insertColumn() (bcftbx.Spreadsheet.Worksheet method) is_absolute (bcftbx.utils.Symlink property) is_boxplot() (in module bcftbx.qc.report)

is_broken (bcftbx.utils.Symlink property) is_dir (bcftbx.utils.PathInfo property) is_empty (bcftbx.qc.report.IlluminaQCSample property) is_executable (bcftbx.utils.PathInfo property) is_fastq_screen() (in module bcftbx.qc.report) is_fastqc() (in module bcftbx.qc.report) is_file (bcftbx.utils.PathInfo property) is_float() (in module bcftbx.simple_xls) is_full (bcftbx.simple_xls.CellIndex property) is_group_readable (bcftbx.utils.PathInfo property) is_group_writable (bcftbx.utils.PathInfo property) is_gzipped_file() (in module bcftbx.utils) is_int() (in module bcftbx.simple_xls) is_link (bcftbx.utils.PathInfo property) is_pair_of() (bcftbx.FASTQFile.SequenceIdentifier method) is_paired_end() (in module bcftbx.SolidData) is_program_info() (in module bcftbx.qc.report) is_readable (bcftbx.utils.PathInfo property) isRunning() (bcftbx.JobRunner.GEJobRunner method) (bcftbx.JobRunner.SimpleJobRunner method) (bcftbx.JobRunner.SlurmRunner method)

J

Job (class in bcftbx.Pipeline)

L

last_column (bcftbx.simple_xls.XLSWorkSheet property) last_row (bcftbx.simple_xls.XLSWorkSheet property) Limits (class in bcftbx.simple_xls) lineno() (bcftbx.TabFile.TabDataLine method) LinkNames (class in bcftbx.Experiment) links() (in module bcftbx.utils)

list_commands() (bcftbx.cmdparse.CommandParser method) list_dirs() (in module bcftbx.utils) list_platforms() (in module bcftbx.platforms) logFile() (bcftbx.JobRunner.GEJobRunner method) (bcftbx.JobRunner.SimpleJobRunner method) (bcftbx.JobRunner.SlurmRunner method) lookup() (bcftbx.TabFile.TabFile method)

M

match() (in module bcftbx.SolidData) md5_walk() (bcftbx.Md5sum.Md5Checker class method) Md5Checker (class in bcftbx.Md5sum) Md5CheckReporter (class in bcftbx.Md5sum) md5cmp_dirs() (bcftbx.Md5sum.Md5Checker class method) md5cmp_files() (bcftbx.Md5sum.Md5Checker class method) md5sum() (in module bcftbx.Md5sum) mkdir() (in module bcftbx.utils) mklink() (in module bcftbx.utils) module bcftbx.cmdparse bcftbx.Experiment bcftbx.FASTQFile bcftbx.htmlpagewriter bcftbx.IlluminaData bcftbx.JobRunner bcftbx.Md5sum bcftbx.ngsutils bcftbx.Pipeline bcftbx.platforms bcftbx.qc.report bcftbx.simple_xls bcftbx.SolidData bcftbx.Spreadsheet bcftbx.TabFile bcftbx.utils

mtime (bcftbx.utils.PathInfo property)

N

n_errors (bcftbx.Md5sum.Md5CheckReporter property) n_failed (bcftbx.Md5sum.Md5CheckReporter property) n_files (bcftbx.Md5sum.Md5CheckReporter property) n_missing (bcftbx.Md5sum.Md5CheckReporter property) n_ok (bcftbx.Md5sum.Md5CheckReporter property) name (bcftbx.qc.report.QCReporter property) (bcftbx.simple_xls.XLSStyle property)

name_matches() (in module bcftbx.utils) nColumns() (bcftbx.TabFile.TabFile method) next() (bcftbx.simple_xls.ColumnRange method) next_column (bcftbx.simple_xls.XLSWorkSheet property) next_row (bcftbx.simple_xls.XLSWorkSheet property) normalise_barcode() (in module bcftbx.IlluminaData) nreads (bcftbx.FASTQFile.FastqAttributes property) nreads() (in module bcftbx.FASTQFile)

O

OrderedDictionary (class in bcftbx.utils)

P

parse_args() (bcftbx.cmdparse.CommandParser method) parser_for() (bcftbx.cmdparse.CommandParser method) path (bcftbx.utils.PathInfo property) PathInfo (class in bcftbx.utils) PipelineRunner (class in bcftbx.Pipeline)

PNGBase64Encoder (class in bcftbx.htmlpagewriter) pretty_print_names() (in module bcftbx.utils) primary_data_dir (bcftbx.qc.report.QCReporter property) print_available_commands() (bcftbx.cmdparse.CommandParser method) print_command() (bcftbx.cmdparse.CommandParser method) programs (bcftbx.qc.report.QCSample property)

Q

qc_dir (bcftbx.qc.report.QCReporter property) QCReporter (class in bcftbx.qc.report)

QCReporterError QCSample (class in bcftbx.qc.report)

R

relpath() (bcftbx.utils.PathInfo method) render_as_text() (bcftbx.simple_xls.XLSWorkSheet method) render_cell() (bcftbx.simple_xls.XLSWorkSheet method) reorderColumns() (bcftbx.TabFile.TabFile method) report() (bcftbx.qc.report.IlluminaQCReporter method) (bcftbx.qc.report.IlluminaQCSample method) (bcftbx.qc.report.QCReporter method) (bcftbx.qc.report.QCSample method) (bcftbx.qc.report.SolidQCReporter method) (bcftbx.qc.report.SolidQCSample method) report_base_name (bcftbx.qc.report.QCReporter property)

report_boxplots() (bcftbx.qc.report.QCSample method) report_fastqc() (bcftbx.qc.report.QCSample method) report_name (bcftbx.qc.report.QCReporter property) report_programs() (bcftbx.qc.report.QCSample method) report_screens() (bcftbx.qc.report.QCSample method) resolve_link_via_parent (bcftbx.utils.PathInfo property) resolve_target() (bcftbx.utils.Symlink method) ResourceLock (class in bcftbx.JobRunner) rootname() (in module bcftbx.utils) row_is_empty() (bcftbx.simple_xls.XLSWorkSheet method) rowof() (bcftbx.simple_xls.XLSWorkSheet method) run (bcftbx.qc.report.QCReporter property)

S

samples (bcftbx.qc.report.QCReporter property) SampleSheet (class in bcftbx.IlluminaData) samplesheet_index_sequence() (in module bcftbx.IlluminaData) save() (bcftbx.Spreadsheet.Workbook method) (bcftbx.Spreadsheet.Worksheet method) save_as_xls() (bcftbx.simple_xls.XLSWorkBook method) save_as_xlsx() (bcftbx.simple_xls.XLSWorkBook method) screens() (bcftbx.qc.report.QCSample method) SequenceIdentifier (class in bcftbx.FASTQFile) set_style() (bcftbx.simple_xls.XLSWorkSheet method) setCellValue() (bcftbx.Spreadsheet.Worksheet method) SimpleJobRunner (class in bcftbx.JobRunner) slide_layout() (in module bcftbx.SolidData) SlurmRunner (class in bcftbx.JobRunner) SolidBarcodeStatistics (class in bcftbx.SolidData) SolidLibrary (class in bcftbx.SolidData) SolidPipelineRunner (class in bcftbx.Pipeline) SolidPrimaryData (class in bcftbx.SolidData) SolidProject (class in bcftbx.SolidData)

SolidQCReporter (class in bcftbx.qc.report) SolidQCSample (class in bcftbx.qc.report) SolidRun (class in bcftbx.SolidData) SolidRunDefinition (class in bcftbx.SolidData) SolidRunInfo (class in bcftbx.SolidData) SolidSample (class in bcftbx.SolidData) sort() (bcftbx.TabFile.TabFile method) split_into_lines() (in module bcftbx.utils) split_run_name() (in module bcftbx.IlluminaData) split_sample_name() (in module bcftbx.qc.report) Spreadsheet (class in bcftbx.Spreadsheet) status (bcftbx.Md5sum.Md5CheckReporter property) strip_ext() (in module bcftbx.utils) strip_ngs_extensions() (in module bcftbx.qc.report) style() (bcftbx.simple_xls.XLSStyle method) Styles (class in bcftbx.Spreadsheet) subset() (bcftbx.TabFile.TabDataLine method) summarise_projects() (in module bcftbx.IlluminaData) summary() (bcftbx.Md5sum.Md5CheckReporter method) Symlink (class in bcftbx.utils)

T

TabDataLine (class in bcftbx.TabFile) TabFile (class in bcftbx.TabFile) TabFileIterator (class in bcftbx.TabFile)

target (bcftbx.utils.Symlink property) touch() (in module bcftbx.utils) transformColumn() (bcftbx.TabFile.TabFile method) transpose() (bcftbx.TabFile.TabFile method)

U

uid (bcftbx.utils.PathInfo property)

update_target() (bcftbx.utils.Symlink method) user (bcftbx.utils.PathInfo property)

V

verify() (bcftbx.qc.report.IlluminaQCSample method) (bcftbx.qc.report.QCReporter method) (bcftbx.qc.report.QCSample method) (bcftbx.qc.report.SolidQCReporter method) (bcftbx.qc.report.SolidQCSample method)

verify_md5sums() (bcftbx.Md5sum.Md5Checker class method) verify_run_against_sample_sheet() (in module bcftbx.IlluminaData)

W

walk() (bcftbx.Md5sum.Md5Checker class method) (in module bcftbx.utils) Workbook (class in bcftbx.Spreadsheet) Worksheet (class in bcftbx.Spreadsheet)

write() (bcftbx.htmlpagewriter.HTMLPageWriter method) (bcftbx.Spreadsheet.Spreadsheet method) (bcftbx.TabFile.TabFile method) write_column() (bcftbx.simple_xls.XLSWorkSheet method) write_row() (bcftbx.simple_xls.XLSWorkSheet method)

X

XLSColumn (class in bcftbx.simple_xls) XLSLimits (class in bcftbx.simple_xls) XLSStyle (class in bcftbx.simple_xls)

XLSWorkBook (class in bcftbx.simple_xls) XLSWorkSheet (class in bcftbx.simple_xls) XLSXLimits (class in bcftbx.simple_xls)

Z

zip() (bcftbx.qc.report.IlluminaQCReporter method) (bcftbx.qc.report.QCReporter method)

zip_includes() (bcftbx.qc.report.QCSample method)