seglh-naming

This repository contains libraries that build, read and validate SEGLH sample/analysis naming conventions.

Installation

The repository provides a python package which can be installed with:

python setup.py install

NB: Use the --user flag or install into an virtualenv/pipenv if not installing globally.

Contributions

Any contributions must follow GIT-Flow. Code reviews are mandatory and must be done by a representative of each site implementing the naming scheme.

A full test suite is provided and can be run with pytest -v. Code formatting must follow recommendations of PEP8. Both requirements are checked automatically via GitHub Actions on pushes to develop and main branches

Naming schemes

After installation the package can be used to validate the folling naming schemes.

Sample

The sample names are structured as follows and can be accessed by the correponding class property.

NGS123_12_382398_P9392B_JD_M_VCP0R33_Pan0000_RJZ_S12_R1_001.realigned.bam
+===== += +===== +===== += + +====== +====== +== +== += +==+=============
|      |  |      |      |  | |       |       |   |   |  |  |
|      |  |      |      |  | |       |       |   |   |  |  +- rest (trailing string, optional)
|      |  |      |      |  | |       |       |   |   |  +---- stable (not informative, optional)
|      |  |      |      |  | |       |       |   |   +------- readnumber (optional)
|      |  |      |      |  | |       |       |   +----------- samplesheetindex (optional)
|      |  |      |      |  | |       |       +--------------- ods (ODS code, optional)
|      |  |      |      |  | |       +----------------------- panelnumber (Pan Number)
|      |  |      |      |  | +------------------------------- panelname (Human readable Pan number)
|      |  |      |      |  +--------------------------------- sex (optional)
|      |  |      |      +------------------------------------ initials (secondary identifier, optional)
|      |  |      +------------------------------------------- id2 (secondary identifier, optional)
|      |  +-------------------------------------------------- id1 (DNA number)
|      +----------------------------------------------------- samplecount (number in batch/library)
+------------------------------------------------------------ libraryprep (library name)

Validation

Validate a sample name or file name for conformity (formatting, required identifiers). If validation fails, a ValueError exception is raised.

from seglh_naming.sample import Sample

# validate sample name
sample = Sample('NGS123_12_382398_JD_M_VCP0R33_Pan0000_S12_R1_001')

# build and validate from the constituent parts
sample = Sample({
	"libraryprep": "NGS123",
	"samplecount": 12,
	"id1": "382398",
	"initials":	"JD",
	"sex": "M",
	"panelname": "VCP0R33",
	"panelnumber": "Pan0000"
})

sample = Sample('NGS123_12_382398_JD_C_VCP0R33_Pan0000_S12_R1_001')
# ValueError: Sex invalid (C)

Sample ID and constituent parts

Get the minimal required Sample ID from filename.

from seglh_naming.sample import Sample

sample = Sample('NGS123_12_382398_JD_M_VCP0R33_Pan0000_S12_R1_001.realigned.bam')

print(sample)
# NGS123_12_382398_JD_M_VCP0R33_Pan0000

print(sample)
# NGS123_12_382398_JD_M_VCP0R33_Pan0000

print(repr(sample))
# NGS123_12_382398_JD_M_VCP0R33_Pan0000_S12_R1_001

Get or edit constituents of sample ID

from seglh_naming.sample import Sample

sample = Sample('NGS123_12_382398_JD_M_VCP0R33_Pan0000_S12_R1_001')

sample.id1
# 382398

sample.id1 = '000111'

print(sample)
# NGS123_12_000111_JD_M_VCP0R33_Pan0000

print(sample.is_modified)
# True

Deidentify

Returns a stable identifier for a given sample ID as a salted, cryptographic hash (SHA256).

from seglh_naming.sample import Sample

print(Sample('NGS123_12_382398_JD_M_VCP0R33_Pan0000_S12_R1_001').hash)
# 998121029e4cd9b64ec7f9218f776255dd16642db498c50e3f2f378153272d84
print(Sample('NGS123_12_382398_JD_M_VCP0R33_Pan0000').hash)
# 998121029e4cd9b64ec7f9218f776255dd16642db498c50e3f2f378153272d84
print(Sample('NGS123_12_382398_JD_M_VCP0R33_Pan0001').hash)
# 9b37c0d8271ca42e5e1067feb22ff3ff2163e549a6094cc2c11ac912d463f07b

File extensions or types

from seglh_naming.sample import Sample

sample = Sample('NGS123_12_382398_JD_M_VCP0R33_Pan0000_S12_R1_001.realigned.vcf.gz')

print(sample.file_extension())
# vcf.gz

print(sample.file_extension(include_compression=False))
# vcf

mduffin95 / seglh-naming