sampleids 0.0.2

Uniform Sample Identifiers Parser

sampleids

Uniform sample ID parser

Available on PyPI at https://pypi.org/project/sampleids/ Available on Github at https://github.com/tmcqueen-materials/sampleids

Quick Start

1. Install: pip3 install sampleids
2. In code, do:

from sampleids import parse as sid_parse, CONFIDENCE as sid_CONFIDENCE

res = sid_parse("AAA_BBB_YYYYMMDD_C_III_S_(QQQQQQQQQQ)-EE", ["AAA",...], ["BBB",...], ["III",...])
print(res) # will print the tuple SampleID(lab_id='AAA', tool_id='BBB', date='20241001', sample_id='C', provenance_id=['III'], split_id='S', parents=[SampleID(lab_id='', tool_id='', date='', sample_id='', provenance_id=[], split_id='', parents=[], extra='', raw='QQQQQQQQQQ', confidence=<CONFIDENCE.NONE: 0>, why='P_PARENT1_PI_V1_6L01_PI_V1_NOPARSE')], extra='EE', raw='AAA_BBB_20241001_C_III_S_(QQQQQQQQQQ)-EE', confidence=<CONFIDENCE.HIGH: 3>, why='P_PARENT1_PI_V1_6L01')

# You can check if confidence is greater than a minimum value, e.g.:
if res.confidence > sid_CONFIDENCE.LOW:
  print("Confidence is not low!")

# The "why" string gives a log of the code paths taken by the parser.
# If you find a case that fails to parse, and you think it should,
# or a case it parses incorrectly, be sure to include the why string!
print(res.why) # prints 'P_PARENT1_PI_V1_6L01'

Specification

This module parses sample identifiers following the schema described at https://occamy.chemistry.jhu.edu/references/samples/index.php . It is a lenient parser, to account for variations observed in the real world, e.g. swapping of month and date, or swapping of identifier fragments.

Version Compatibility

sampleids is compatible with all versions of Python 3.4+.