genomics-bcftbx
latest
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
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
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 property)
datetime (bcftbx.utils.PathInfo property)
deepest_accessible_parent (bcftbx.utils.PathInfo property)
delimiter() (bcftbx.TabFile.TabDataLine method)
describe() (bcftbx.Experiment.Experiment method)
describe_project() (in module bcftbx.IlluminaData)
dirn (bcftbx.qc.report.QCReporter property)
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 property)
exists (bcftbx.utils.PathInfo property)
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 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
ge_extra_args (bcftbx.JobRunner.GEJobRunner property)
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_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 property)
isRunning() (bcftbx.JobRunner.BaseJobRunner 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() (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 property)
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)
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() (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 property)
next_row (bcftbx.simple_xls.XLSWorkSheet property)
normalise_barcode() (in module bcftbx.IlluminaData)
nreads (bcftbx.FASTQFile.FastqAttributes property)
nreads() (in module bcftbx.FASTQFile)
nslots (bcftbx.JobRunner.GEJobRunner property)
(bcftbx.JobRunner.SimpleJobRunner property)
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)
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 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)
run() (bcftbx.JobRunner.BaseJobRunner method)
(bcftbx.JobRunner.GEJobRunner method)
(bcftbx.JobRunner.SimpleJobRunner method)
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_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 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)
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 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)
Read the Docs
v: latest
Versions
latest
stable
devel
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds