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mcmero / SVclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
BSD 3-Clause "New" or "Revised" License
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AttributeError when combining ccube_sv_input files #27

Closed mdiaz09 closed 1 year ago

mdiaz09 commented 1 year ago

Similar to #10 I am interested in analyzing paired samples but am having trouble running the clustering function with the combined input. I combined the two ccube_sv_input files and averaged the refcounts. I encountered the following error when running SVclone cluster AttributeError: 'DataFrame' object has no attribute 'gtype1' Is this error due to missing or malformed inputs?

Thank you in advance,

Mike

mdiaz09 commented 1 year ago

I misunderstood the conversation in #10, ccube_sv_input is used as an input for pyclone, not ccube. The filtered_svs.tsv dataset is the input for ccube and one column is named gtype1.

mcmero commented 1 year ago

Just to clarify, the filtered_svs.tsv file is used as input to SVclone's cluster step, and is converted to a ccube_sv_input.txt file as input for ccube clustering (this is an internal step and occurs due to legacy reasons). In #10, the user asked about converting this input file into PyClone input, as SVclone does not support paired-sample clustering.