dfornika / miseq-samplesheet-parser

Parse illumina MiSeq SampleSheet.csv files and convert to JSON

MiSeq SampleSheet.csv Parser

Parse illumina MiSeq SampleSheet.csv files and convert to JSON

Usage

samplesheet_parser.py SampleSheet.csv

samplesheet_parser.py SampleSheet.csv | python -m json.tool

Example Input & Output

Input

[Header]
IEMFileVersion,5
Investigator Name,Dr. Sequencer
Experiment Name,Truly Insightful Experiment
Date,10/08/2020
Workflow,GenerateFASTQ
Application,FASTQ Only
Instrument Type,MiSeq
Assay,Nextera DNA Flex
Index Adapters,Nextera DNA CD Indexes (96 Indexes plated)
Description,Our most precious samples
Chemistry,Amplicon
[Reads]
251
251
[Settings]
ReverseComplement,0
Adapter,CTGTCTCTTATACACATCT
[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Index_Plate_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
S1,SAMPLE_01,,,A01,H701,TAAGGCGA,H505,GTAAGGAG,,,
S2,SAMPLE_02,,,B01,H702,CGTACTAG,H517,GCGTAAGA,,,

Output

{
    "header": {
        "iemfileversion": "5",
        "investigator_name": "Dr. Sequencer",
        "experiment_name": "Truly Insightful Experiment",
        "date": "10/08/2020",
        "workflow": "GenerateFASTQ",
        "application": "FASTQ Only",
        "instrument_type": "MiSeq",
        "assay": "Nextera DNA Flex",
        "index_adapters": "Nextera DNA CD Indexes (96 Indexes plated)",
        "description": "Our most precious samples",
        "chemistry": "Amplicon"
    },
    "reads": [
        251,
        251
    ],
    "settings": {
        "adapter": "CTGTCTCTTATACACATCT",
        "reversecomplement": "0"
    }
    "data": [
        {
            "sample_id": "S1",
            "sample_name": "SAMPLE_01",
            "sample_plate": "",
            "sample_well": "",
            "index_plate_well": "A01",
            "i7_index_id": "H701",
            "index": "TAAGGCGA",
            "i5_index_id": "H505",
            "index2": "GTAAGGAG",
            "sample_project": "",
            "description": ""
        },
        {
            "sample_id": "S2",
            "sample_name": "SAMPLE_02",
            "sample_plate": "",
            "sample_well": "",
            "index_plate_well": "B01",
            "i7_index_id": "H702",
            "index": "CGTACTAG",
            "i5_index_id": "H517",
            "index2": "GCGTAAGA",
            "sample_project": "",
            "description": ""
        }
    ]
}