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https://github.com/dfornika/miseq-samplesheet-parser
Parse illumina MiSeq SampleSheet.csv files and convert to JSON
https://github.com/dfornika/miseq-samplesheet-parser
bioinformatics illumina miseq next-generation-sequencing
Last synced: 28 days ago
JSON representation
Parse illumina MiSeq SampleSheet.csv files and convert to JSON
- Host: GitHub
- URL: https://github.com/dfornika/miseq-samplesheet-parser
- Owner: dfornika
- Created: 2020-09-11T00:49:27.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-10-01T18:26:51.000Z (about 4 years ago)
- Last Synced: 2024-10-14T15:26:42.105Z (2 months ago)
- Topics: bioinformatics, illumina, miseq, next-generation-sequencing
- Language: Python
- Homepage:
- Size: 4.88 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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": ""
}
]
}
```