Sample-sheet

The validation criteria for sample collisions in the same sample sheet has been adjusted so that you can theoretically have the same `Sample_ID`, `Library_ID`, `index`, and `index2` in the sample sheet as long as they appear in a different `Lane` only.

As requested in 33 by reisingerf.

Round-trip reading, modifying, and writing!
---

Sample sheets will always be written in a deterministc manner which will help with hashing changes.

You can perform a round-trip read, modify, write (example below) or create a sample sheet _de novo_ by instantiating `SampleSheet` and `Sample` classes and modifying them directly as shown in the [README](https://github.com/clintval/sample-sheet#sample-sheet-creation)

python
infile = 'https://raw.githubusercontent.com/clintval/sample-sheet/master/tests/resources/paired-end-single-index.csv'
sample_sheet = SampleSheet(infile)

with open('test.csv', 'w') as handle:
sample_sheet.write(handle)


bash
❯ head <( https://raw.githubusercontent.com/clintval/sample-sheet/master/tests/resources/paired-end-single-index.csv )
[Header],,,,,,,,
IEM1FileVersion,4,,,,,,,
Investigator Name,jdoe,,,,,,,
Experiment Name,exp001,,,,,,,
Date,11/16/2017,,,,,,,
Workflow,SureSelectXT,,,,,,,
Application,NextSeq FASTQ Only,,,,,,,
Assay,SureSelectXT,,,,,,,
Description,A description of this flow cell,,,,,,,
Chemistry,Default,,,,,,,



bash
❯ head test.csv
[Header],,,,,,,,
IEM1FileVersion,4,,,,,,,
Investigator Name,jdoe,,,,,,,
Experiment Name,exp001,,,,,,,
Date,11/16/2017,,,,,,,
Workflow,SureSelectXT,,,,,,,
Application,NextSeq FASTQ Only,,,,,,,
Assay,SureSelectXT,,,,,,,
Description,A description of this flow cell,,,,,,,
Chemistry,Default,,,,,,,


Test Coverage CI
---

Code test coverage is now calculated on all branches and PRs.

Goal for this project will be sustaining at least 95% coverage with a target of 100%.

https://codecov.io/gh/clintval/sample-sheet

- 100% test coverage and [CI integration](https://travis-ci.org/clintval/sample-sheet/) :


❯ ./sample-sheet/run-tests
Name Stmts Miss Cover
---------------------------------------------------
sample_sheet/__init__.py 1 0 100%
sample_sheet/_sample_sheet.py 280 0 100%
---------------------------------------------------
TOTAL 281 0 100%

OK! 58 tests, 0 failures, 0 errors in 0.0s


- Print ASCII or HTML (IPython auto-detected) summaries of samples:

python
>>> sample_sheet.experimental_design
"""
| sample_id | sample_name | library_id | description |
|:------------|:--------------|:-------------|:-----------------|
| 1823A | 1823A-tissue | 2017-01-20 | 0.5x treatment |
| 1823B | 1823B-tissue | 2017-01-20 | 0.5x treatment |


- Get rich unicode CLI summaries of sample sheets:

bash
❯ sample-sheet-summary paired-end-single-index.csv
┌Header─────────────┬─────────────────────────────────┐
│ iem1_file_version │ 4 │
│ investigator_name │ jdoe │
│ experiment_name │ exp001 │
│ date │ 11/16/2017 │
│ workflow │ SureSelectXT │
│ application │ NextSeq FASTQ Only │
│ assay │ SureSelectXT │
│ description │ A description of this flow cell │
│ chemistry │ Default │
└───────────────────┴─────────────────────────────────┘
...

- README in ReStructered format, PyPi still garbles it.
- `extras_require` now works with

bash
$ pip install '.[test]'

Features:
- Supports [Header], [Settings], [Reads], and [Data] sections of Illumina sample sheets
- Uses `smart_open` to open a file on S3, HDFS, WebHDFS, HTTP as well as local (compressed or not)
- If a `Read_Structure` column can be inferred, then the structure is promoted to class `ReadStructure`.

Known bugs:
- Script to output sample-sheet in terminal doesn't quite work yet.
- `experimental_design()` was irreparably broken
- Interface for barcode and library parameter generating methods were left behind.