sample-sheet 0.0.2

An Illumina Sample Sheet parsing utility.

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sample-sheet

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A Python 3.6 library for handling Illumina sample sheets

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Installation · Examples · Command Line Tools · Contributing

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Installation

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Until this package is released on PyPi, one can install directly from
the ``master`` branch with the following command:

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❯ pip install [e-mail]:clintval/sample-sheet.git

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Examples

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A sample sheet can be read from S3, HDFS, WebHDFS, HTTP as well as local
(compressed or not).

.. code:: python

>>> from sample_sheet import SampleSheet
>>> SampleSheet('s3://bucket/prefix/SampleSheet.csv')
SampleSheet("s3://bucket/prefix/SampleSheet.csv")

An example sample sheet can be found at
```tests/resources/paired-end-single-index.csv`` <tests/resources/paired-end-single-index.csv>`__.

.. code:: python

>>> from sample_sheet import SampleSheet

>>> infile = 'tests/resources/paired-end-single-index.csv'
>>> sample_sheet = SampleSheet(infile)

The metadata of the sample sheet can be accessed with the ``header``,
``reads`` and, ``settings`` attributes:

.. code:: python

>>> sample_sheet.header.assay
'SureSelectXT'
>>> sample_sheet.reads
[151, 151]
>>> sample_sheet.is_paired
True
>>> sample_sheet.settings.barcode_mismatches
'2'

The samples can be accessed directly or *via* iteration:

.. code:: python

>>> sample_sheet.samples
[Sample({"index": "GAATCTGA", "sample_id": "1823A", "sample_name": "1823A-tissue"}),
Sample({"index": "AGCAGGAA", "sample_id": "1823B", "sample_name": "1823B-tissue"}),
Sample({"index": "GAGCTGAA", "sample_id": "1824A", "sample_name": "1824A-tissue"}),
Sample({"index": "AAACATCG", "sample_id": "1825A", "sample_name": "1825A-tissue"}),
Sample({"index": "GAGTTAGC", "sample_id": "1826A", "sample_name": "1826A-tissue"}),
Sample({"index": "CGAACTTA", "sample_id": "1826B", "sample_name": "1823A-tissue"}),
Sample({"index": "GATAGACA", "sample_id": "1829A", "sample_name": "1823B-tissue"})]

>>> for sample in sample_sheet:
>>> print(repr(sample)); break
Sample({"index": "GAATCTGA", "sample_id": "1823A", "sample_name": "1823A-tissue"})

If a column name for read structure can be inferred, then additional
functionality is enabled.

.. code:: python

>>> first_sample, *_ = sample_sheet.samples
>>> first_sample.read_structure
ReadStructure(structure="151T8B151T")
>>> first_sample.read_structure.total_cycles
310
>>> first_sample.read_structure.tokens
['151T', '8B', '151T']

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Command Line Tools

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sample-sheet-summary

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`sample-sheet-summary <#sample-sheet-summary>`__
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Prints a unicode table summary of the sample sheet.

Note currently broken. Output below to give you an idea of what the
final result will look like.

.. code:: bash

❯ sample-sheet-summary paired-end-single-index.csv
┌Header─────────────┬──┐
│ IEM1FileVersion │ │
│ Investigator Name │ │
│ Experiment Name │ │
│ Date │ │
│ Workflow │ │
│ Application │ │
│ Assay │ │
│ Description │ │
│ Chemistry │ │
└───────────────────┴──┘
┌Settings──────────────────┬──────────┐
│ CreateFastqForIndexReads │ │
│ BarcodeMismatches │ │
│ Reads │ 151, 151 │
└──────────────────────────┴──────────┘
┌Identifiers┬──────────────┬────────────┬─────────────┬──────────┬─────────────┬────────┐
│ sample_id │ sample_name │ library_id │ i7_index_id │ index │ i5_index_id │ index2 │
├───────────┼──────────────┼────────────┼─────────────┼──────────┼─────────────┼────────┤
│ 1823A │ 1823A-tissue │ 2017-01-20 │ │ GAATCTGA │ │ │
│ 1823B │ 1823B-tissue │ 2017-01-20 │ │ AGCAGGAA │ │ │
│ 1824A │ 1824A-tissue │ 2017-01-20 │ │ GAGCTGAA │ │ │
│ 1825A │ 1825A-tissue │ 2017-01-20 │ │ AAACATCG │ │ │
│ 1826A │ 1826A-tissue │ 2017-01-20 │ │ GAGTTAGC │ │ │
│ 1826B │ 1823A-tissue │ 2017-01-17 │ │ CGAACTTA │ │ │
│ 1829A │ 1823B-tissue │ 2017-01-17 │ │ GATAGACA │ │ │
└───────────┴──────────────┴────────────┴─────────────┴──────────┴─────────────┴────────┘

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Contributing

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Pull requests and issues welcome! Before submitting a pull request
please ensure your code is tested and that the tests run OK. To use the
helper function ``run-tests`` you must have the test libraries
installed. A development install also helps:

.. code:: bash

❯ git clone [e-mail]:clintval/sample-sheet.git
❯ pip install -e sample-sheet\[test\]

To run the tests:

::

❯ ./sample-sheet/run-tests
Name Stmts Miss Cover
---------------------------------------------------
sample_sheet/__init__.py 1 0 100%
sample_sheet/_sample_sheet.py 272 10 96%
---------------------------------------------------
TOTAL 273 10 96%

OK! 47 tests, 0 failures, 0 errors in 0.0s