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Verify image_gene_node_attributes.tsv generation is valid #1

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coleslaw481 opened this issue May 9, 2023 · 0 comments
Open

Verify image_gene_node_attributes.tsv generation is valid #1

coleslaw481 opened this issue May 9, 2023 · 0 comments
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@coleslaw481
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Double check we are generating this output correctly.

For example here is samples fragment:

filename,if_plate_id,position,sample,status,locations,antibody,ensembl_ids,gene_names
/archive/1270/1270_C11_1_,1270,C11,1,35,"Nucleoli,Nucleoplasm",HPA068294,"ENSG00000116251,ENSG00000163584","RPL22,RPL22L1"
/archive/1270/1270_C11_2_,1270,C11,2,35,"Nucleoli,Nucleoplasm",HPA068294,"ENSG00000116251,ENSG00000163584","RPL22,RPL22L1"
/archive/1542/1542_A12_1_,1542,A12,1,35,Nucleoli,HPA048060,ENSG00000163584,RPL22L1
/archive/1542/1542_A12_2_,1542,A12,2,35,Nucleoli,HPA048060,ENSG00000163584,RPL22L1

and here is unique fragment:

antibody,ensembl_ids,gene_names,atlas_name,locations,n_location
HPA068294,"ENSG00000116251,ENSG00000163584","RPL22,RPL22L1",U-2 OS,"Nucleoli,Nucleoplasm",2
HPA048060,ENSG00000163584,RPL22L1,U-2 OS,Nucleoli,1

For version 0.1.0 the resulting image_gene_node_attributes.tsv contains this:

name	represents	ambiguous	antibody	filename
RPL22L1	ensembl:ENSG00000163584	RPL22,RPL22L1	HPA068294,HPA048060	1542_A12_2_,1542_A12_1_,1270_C11_2_,1270_C11_1_
RPL22	ensembl:ENSG00000116251	RPL22,RPL22L1	HPA068294	1270_C11_2_,1270_C11_1_

The original jupyter notebook implementation kicked out this for image_gene_node_attributes.tsv:

name	represents	ambiguous	antibody	filename
RPL22	ensembl:ENSG00000116251	RPL22,RPL22L1	HPA068294	1270_C11_1_
RPL22L1	ensembl:ENSG00000163584	RPL22,RPL22L1	HPA048060	1542_A12_1_

Are we wrong or is the jupyter notebook implementation wrong?

@coleslaw481 coleslaw481 added the bug Something isn't working label May 9, 2023
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