search

barkasn / scAlleleCount

4 stars 1 forks source link

Matrix output issue #8

Open ljmfong opened 5 months ago

ljmfong commented 5 months ago

Hi!

I've been trying to run scAlleleCount.py for an analysis and the python script seems to be running fine, here is the verbose output:

reading snps file... done building positions index... done reading barcodes file... reading barcodes file... done building barcodes index... done perfoming pileup.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................done saving matrices...done

However, all three matrices have a weird output, example here:

%%MatrixMarket matrix coordinate integer general % 1718060 532746 0

My barcode file contains only unique barcodes. I saw some responses that suggest using wrapperfunction.R but I'm having issues with R that may take some time to fix and would like to try to run the python script in the command line in the mean time.

Thank you for any help!