genomics-bcftbx
devel
Getting started
Overview
Requirements
Installation
Background
Illumina sequencing data
SOLiD sequencing data
Usage
Handling sequencing run data
NGS utilities
Fastq manipulation
Fasta manipulation
Microarray data
Non-bioinformatics utilities
Utilities
Command reference
bcftbx Library
bcftbx
library reference
Version History and Changes
genomics-bcftbx
Docs
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Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Z
A
acquire() (bcftbx.JobRunner.ResourceLock method)
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)
copy() (bcftbx.Experiment.Experiment method)
count_reads() (in module bcftbx.qc.report)
D
data_format (bcftbx.qc.report.QCReporter attribute)
datetime (bcftbx.utils.PathInfo attribute)
deepest_accessible_parent (bcftbx.utils.PathInfo attribute)
delimiter() (bcftbx.TabFile.TabDataLine method)
describe() (bcftbx.Experiment.Experiment method)
describe_project() (in module bcftbx.IlluminaData)
dirn (bcftbx.qc.report.QCReporter attribute)
dirname() (bcftbx.Experiment.Experiment method)
E
encodePNG() (bcftbx.htmlpagewriter.PNGBase64Encoder method)
errFile() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner method)
error() (bcftbx.cmdparse.CommandParser method)
errorState() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
eval_formula() (in module bcftbx.simple_xls)
excel_number_format (bcftbx.simple_xls.XLSStyle attribute)
exists (bcftbx.utils.PathInfo attribute)
exit_status() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner method)
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 attribute)
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 attribute)
format_file_size() (in module bcftbx.utils)
format_value() (in module bcftbx.simple_xls)
freezePanes() (bcftbx.Spreadsheet.Worksheet method)
fsize (bcftbx.FASTQFile.FastqAttributes attribute)
full_index() (bcftbx.simple_xls.XLSColumn method)
G
ge_extra_args (bcftbx.JobRunner.GEJobRunner attribute)
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_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 attribute)
group (bcftbx.utils.PathInfo attribute)
H
handle_generic_commands() (bcftbx.cmdparse.CommandParser method)
header() (bcftbx.TabFile.TabFile method)
html (bcftbx.qc.report.QCReporter attribute)
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 attribute)
is_boxplot() (in module bcftbx.qc.report)
is_broken (bcftbx.utils.Symlink attribute)
is_dir (bcftbx.utils.PathInfo attribute)
is_empty (bcftbx.qc.report.IlluminaQCSample attribute)
is_executable (bcftbx.utils.PathInfo attribute)
is_fastq_screen() (in module bcftbx.qc.report)
is_fastqc() (in module bcftbx.qc.report)
is_file (bcftbx.utils.PathInfo attribute)
is_float() (in module bcftbx.simple_xls)
is_full (bcftbx.simple_xls.CellIndex attribute)
is_group_readable (bcftbx.utils.PathInfo attribute)
is_group_writable (bcftbx.utils.PathInfo attribute)
is_gzipped_file() (in module bcftbx.utils)
is_int() (in module bcftbx.simple_xls)
is_link (bcftbx.utils.PathInfo attribute)
is_locked() (bcftbx.JobRunner.ResourceLock method)
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 attribute)
isRunning() (bcftbx.JobRunner.BaseJobRunner method)
J
Job (class in bcftbx.Pipeline)
L
last_column (bcftbx.simple_xls.XLSWorkSheet attribute)
last_row (bcftbx.simple_xls.XLSWorkSheet attribute)
Limits (class in bcftbx.simple_xls)
lineno() (bcftbx.TabFile.TabDataLine method)
LinkNames (class in bcftbx.Experiment)
links() (in module bcftbx.utils)
list() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner method)
list_commands() (bcftbx.cmdparse.CommandParser method)
list_dirs() (in module bcftbx.utils)
list_platforms() (in module bcftbx.platforms)
log_dir (bcftbx.JobRunner.BaseJobRunner attribute)
logFile() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner 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)
mtime (bcftbx.utils.PathInfo attribute)
N
n_errors (bcftbx.Md5sum.Md5CheckReporter attribute)
n_failed (bcftbx.Md5sum.Md5CheckReporter attribute)
n_files (bcftbx.Md5sum.Md5CheckReporter attribute)
n_missing (bcftbx.Md5sum.Md5CheckReporter attribute)
n_ok (bcftbx.Md5sum.Md5CheckReporter attribute)
name (bcftbx.qc.report.QCReporter attribute)
(bcftbx.simple_xls.XLSStyle attribute)
name() (bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner method)
name_matches() (in module bcftbx.utils)
names() (bcftbx.Experiment.LinkNames method)
nColumns() (bcftbx.TabFile.TabFile method)
next() (bcftbx.simple_xls.ColumnRange method)
next_column (bcftbx.simple_xls.XLSWorkSheet attribute)
next_row (bcftbx.simple_xls.XLSWorkSheet attribute)
normalise_barcode() (in module bcftbx.IlluminaData)
nreads (bcftbx.FASTQFile.FastqAttributes attribute)
nreads() (in module bcftbx.FASTQFile)
nslots (bcftbx.JobRunner.GEJobRunner attribute)
(bcftbx.JobRunner.SimpleJobRunner attribute)
O
OrderedDictionary (class in bcftbx.utils)
P
parse_args() (bcftbx.cmdparse.CommandParser method)
parser_for() (bcftbx.cmdparse.CommandParser method)
path (bcftbx.utils.PathInfo attribute)
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 attribute)
print_available_commands() (bcftbx.cmdparse.CommandParser method)
print_command() (bcftbx.cmdparse.CommandParser method)
programs (bcftbx.qc.report.QCSample attribute)
Q
qc_dir (bcftbx.qc.report.QCReporter attribute)
QCReporter (class in bcftbx.qc.report)
QCReporterError
QCSample (class in bcftbx.qc.report)
queue() (bcftbx.JobRunner.GEJobRunner method)
R
release() (bcftbx.JobRunner.ResourceLock method)
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 attribute)
report_boxplots() (bcftbx.qc.report.QCSample method)
report_fastqc() (bcftbx.qc.report.QCSample method)
report_name (bcftbx.qc.report.QCReporter attribute)
report_programs() (bcftbx.qc.report.QCSample method)
report_screens() (bcftbx.qc.report.QCSample method)
resolve_link_via_parent (bcftbx.utils.PathInfo attribute)
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 attribute)
run() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner method)
S
samples (bcftbx.qc.report.QCReporter attribute)
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_log_dir() (bcftbx.JobRunner.BaseJobRunner method)
set_style() (bcftbx.simple_xls.XLSWorkSheet method)
setCellValue() (bcftbx.Spreadsheet.Worksheet method)
SimpleJobRunner (class in bcftbx.JobRunner)
slide_layout() (in module bcftbx.SolidData)
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 attribute)
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 attribute)
terminate() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner method)
touch() (in module bcftbx.utils)
transformColumn() (bcftbx.TabFile.TabFile method)
transpose() (bcftbx.TabFile.TabFile method)
U
uid (bcftbx.utils.PathInfo attribute)
update_target() (bcftbx.utils.Symlink method)
user (bcftbx.utils.PathInfo attribute)
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)
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