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gaolabtools / scNanoGPS

Single cell Nanopore sequencing data for Genotype and Phenotype
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Weird behaviour - assigner.py #3

Closed davidebolo1993 closed 1 year ago

davidebolo1993 commented 1 year ago

Hi,

it seems assigner.py combines somehow the output folder with the input file to look for the barcode list. Minimal example:

python3 resources/scNanoGPS/assigner.py -i evaluation/scanner/barcode_list.tsv.gz

returns

Cannot find Cell barcode list file: scNanoGPS_res/evaluation/scanner/barcode_list.tsv.gz !

Workaround is copy the barcode_list.tsv.gz in the output folder and run assigner from the output folder itself - but this is something I don't want to use in the long-term.

Thx,

Davide

shiauck commented 1 year ago

Hi Davide,

When using the assigner parameter "-i", you only need to give "barcode_list.tsv.gz" as default. Because your working folder is at "evaluation/scanner", please give the folder name with "-o" parameter. In your case, it could be "-o evaluation/scanner". Assigner will assemble the two parameters together to fetch the input file from "/evaluation/scanner/barcode_list.tsv.gz"

If you feel like to separate outputs step-by-step, you can consider using symbolic link to play the trick without changing the meta file name but the folder name.

Thank you for feedback. Cheng-Kai