Multiple samples with same index

[nuin]

When opening a SampleSheet with multiple samples with the same index (usual for me), where the final index for the sample is determined by the pair and not by uniqueness of each single index, we get an ValueError:

ValueError: Sample index combination for XX-XX-4Y has already been added: XX-XX-5G

It would be good to allow for share indexes among samples.

[nuin]

In my case the first sample XX-XX-4Y has indexes N701 and E502, while the other sample has N701 and E506.

[clintval]

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?

[nuin]

I will remove some sensitive information and paste it here.

[clintval]

Thanks! Much appreciated.

[clintval]

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.

[nuin]

OK, thanks, I will paste anyway. Seems to be here:

sample-sheet/sample_sheet/_sample_sheet.py

Line 468 in d80acf9

if (

[nuin]

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,,```

[clintval]

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.git

[clintval]

Try now. I did test on your example sheet with no problems.

$ pip3 install sample_sheet

Newest release v0.2.0 is up on PyPi. https://pypi.python.org/pypi/sample_sheet

[nuin]

I will check, thanks a lot.