Sample-sheet

Breaking

To make use of the `smart_open` library, simply install it alongside `sample-sheet` as it is no longer vendored here.

- Support for redundant `Sample_ID` with warning
- Ordered output of sample headers in `.write()` as they were read-in or assigned
- Case insensitive hashing for sample attributes

Specifically formats with:

- blank lines
- non-comma terminated lines

Feature request from andybearman

You can now do:

python
content = SampleSheet(filename).to_json()


And on the CLI:

bash
❯ sample-sheet to_json paired-end-single-index.csv | jq
{
"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"
},
"Reads": [
151,
151
],
"Settings": {
"CreateFastqForIndexReads": "1",
"BarcodeMismatches": "2"
},
"Data": [
{
"Sample_Project": "exp001",
"Description": "0.5x treatment",
"Reference_Name": "mm10",
"Sample_Name": "1823A-tissue",
"index": "GAATCTGA",
"Library_ID": "2017-01-20",
"Read_Structure": "151T8B151T",
"Sample_ID": "1823A",
"Target_Set": "Intervals-001"
},
...
]
}

We now adhere to the entire Illumina specification for sample sheets and support many short-read analysis platform sample sheet variants including NextSeq, TrueSeq, and NovaSeq.

Example of adding a user-defined section thanks to help from slagelwa:

python
from sample_sheet import SampleSheet

sample_sheet = SampleSheet()
sample_sheet.add_section('Manifests')

Add a key value pair!
sample_sheet.Manifests.Key1 = "value1"


The `.write()` method will write each section out in the order they are defined between the `[Reads]` and `[Settings]` sections.