Comments (10)
clintval
commented on June 24, 2024
1
Fixed in #10.
I will make a new release later today on PyPi but in the meantime you can either check out the master branch and install or do:
$ pip install git+git://github.com/clintval/sample-sheet.gitfrom sample-sheet.
nuin
commented on June 24, 2024
In my case the first sample XX-XX-4Y has indexes N701 and E502, while the other sample has N701 and E506.
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clintval
commented on June 24, 2024
Would it be possible for you to send me a simple example of your sample sheet to test on? Are your index fields index and index2?
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nuin
commented on June 24, 2024
I will remove some sensitive information and paste it here.
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clintval
commented on June 24, 2024
Thanks! Much appreciated.
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clintval
commented on June 24, 2024
This is a bug. I see it now in the code.
I can fix it later today and push to GiHub after unit testing. Then you should be able to install off the master branch and use the fix.
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nuin
commented on June 24, 2024
OK, thanks, I will paste anyway. Seems to be here:
sample-sheet/sample_sheet/_sample_sheet.py
Line 468 in d80acf9
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nuin
commented on June 24, 2024
Sample sheet is this
[Header],,,,,,,,,,
IEMFileVersion,4,,,,,,,,,
Investigator Name,0,,,,,,,,,
Experiment Name,run_02_2018,,,,,,,,,
Date,12/01/2018,,,,,,,,,
Workflow,GenerateFASTQ,,,,,,,,,
Application,NextSeq FASTQ Only,,,,,,,,,
Assay,Nextera Rapid Capture Enrichment,,,,,,,,,
Description,,,,,,,,,,
Chemistry,Amplicon,,,,,,,,,
,,,,,,,,,,
[Reads],,,,,,,,,,
151,,,,,,,,,,
151,,,,,,,,,,
,,,,,,,,,,
[Settings],,,,,,,,,,
Adapter,CTGTCTCTTATACACATCT,,,,,,,,,
,,,,,,,,,,
[Data],,,,,,,,,,
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,GenomeFolder,Sample_Project,Description
sample 1,sample 1,run_02_2018,A01,N701,TAAGGCGA,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 2,sample 2,run_02_2018,A02,N702,CGTACTAG,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 3,sample 3,run_02_2018,A03,N703,AGGCAGAA,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 4,sample 4,run_02_2018,A04,N704,TCCTGAGC,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 5,sample 5,run_02_2018,A05,N705,GGACTCCT,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 6,sample 6,run_02_2018,A06,N706,TAGGCATG,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 7,sample 7,run_02_2018,A07,N707,CTCTCTAC,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 8,sample 8,run_02_2018,A08,N708,CAGAGAGG,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 9,sample 9,run_02_2018,A09,N710,CGAGGCTG,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 10,sample 10,run_02_2018,A10,N711,AAGAGGCA,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 11,sample 11,run_02_2018,A11,N712,GTAGAGGA,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 12,sample 12,run_02_2018,A12,N701,TAAGGCGA,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 13,sample 13,run_02_2018,B01,N702,CGTACTAG,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 14,sample 14,run_02_2018,B02,N703,AGGCAGAA,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 15,sample 15,run_02_2018,B03,N704,TCCTGAGC,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 16,sample 16,run_02_2018,B04,N705,GGACTCCT,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 17,sample 17,run_02_2018,B05,N706,TAGGCATG,E502,ATAGAGAG,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 18,sample 18,run_02_2018,B06,N707,CTCTCTAC,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 19,sample 19,run_02_2018,B07,N708,CAGAGAGG,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 20,sample 20,run_02_2018,B08,N710,CGAGGCTG,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 21,sample 21,run_02_2018,B09,N711,AAGAGGCA,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 22,sample 22,run_02_2018,B10,N712,GTAGAGGA,E506,TATGCAGT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 23,sample 23,run_02_2018,B11,N704,TCCTGAGC,E507,TACTCCTT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,
sample 24,sample 24,run_02_2018,B12,N705,GGACTCCT,E507,TACTCCTT,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA,,```
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clintval
commented on June 24, 2024
Try now. I did test on your example sheet with no problems.
$ pip3 install sample_sheetNewest release v0.2.0 is up on PyPi. https://pypi.python.org/pypi/sample_sheet
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nuin
commented on June 24, 2024
I will check, thanks a lot.
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Related Issues (20)
- Support Python2 HOT 1
- Support comments HOT 2
- Feature Request: SampleSheet v2 support HOT 9
- validator HOT 7
- How to update the sample sheet object? HOT 1
- index validation HOT 2
- Intended behavior of empty samplesheet with missing sections HOT 1
- Index validation on indexes with spaces at the end
- Request - handling nonstandard tables HOT 1
- relationship with PEP HOT 1
- Issue1: special character
- Confusing error on file with no sections
- test_to_picard_basecalling_params_output_files fails on MacOS
- Appetite for looking up samples by Sample_ID HOT 1
- Feature request: support read structures like `+T` HOT 1
- PE + Multi index HOT 2
- Add option do deactivate sanity check for reading sample sheets and adding samples
- Sample_ID validation
- Do you support custom application settings and data sections? does Illumina? HOT 1
- Error parsing samplesheet HOT 1
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