Parsing single cell GSE and get series_table

[rjpbonnal]

I can get the usual information from the below GSE but I can not find a way to read the series_table where the authors keep track of each single cell and the groups it belongs to in the downstream analysis.

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98638/soft/GSE98638_family.soft.gz

!series_table_begin = Listing of Individual Cells
UniqueCell_ID   Patient majorCluster    sampleType
NTC148-0322     P0322   C01_CD8-LEF1    NTC
NTC69-0407      P0407   C01_CD8-LEF1    NTC
NTC81-0407      P0407   C01_CD8-LEF1    NTC
NTC96-0407      P0407   C01_CD8-LEF1    NTC
NTC2-55-0508    P0508   C01_CD8-LEF1    NTC
...
TTS5-1202       P1202t  unknown TTR
TTS7-1202       P1202t  unknown TTR
TTS8-1202       P1202t  unknown TTR
!series_table_end

Does the library read this type of annotation ?

[seandavi]

Thanks, @helios. This is apparently a new use of the !series_table in SOFT format for GEO series. I can implement this parsing as a new feature. I don't have a timeframe, though.

[rjpbonnal]

@seandavi ok great. If you have time to give me some hints on how to start hacking the code I can try to implement it by myself and later on provide a merge.