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?
Double check we are generating this output correctly.
For example here is samples fragment:
and here is unique fragment:
For version
0.1.0the resultingimage_gene_node_attributes.tsvcontains this:The original jupyter notebook implementation kicked out this for
image_gene_node_attributes.tsv:Are we wrong or is the jupyter notebook implementation wrong?