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GWW / scsnv

scSNV Mapping tool for 10X Single Cell Data
MIT License
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error in scsnvmisc #9

Closed earn97 closed 2 years ago

earn97 commented 2 years ago

Hi,

Thank you for your amazing tool!

I encountered the error when I did scsnvmisc cells. The code and error is bellow.

scsnvmisc --skip-mt cells -o /home/jhmoon/data/dami/sample /home/jhmoon/data/dami/sample/summary.h5

> Invalid program available options are cells, annotate, cellranger, snv2vcfmtx, merge, results

So I delete '--skip-mt' option, but it still didn't work.

scsnvmisc --skip-mt cells -o /home/jhmoon/data/dami/sample /home/jhmoon/data/dami/sample/summary.h5

> /data/jhmoon/MyLib/anaconda3/lib/python3.9/site-packages/scsnvpy-1.0-py3.9-linux-x86_64.egg/scsnvpy/cells.py:241: MatplotlibDeprecationWarning: The 'subsx' parameter of __init__() has been renamed 'subs' since Matplotlib 3.3; support for the old name will be dropped two minor releases later.
  ax.set_xscale('log', subsx=[2,3,4,5,6,7,8,9])
  Error {key} not in the barcode data columns

Is there any idea that can solve this problem?

GWW commented 2 years ago

Hi,

Your command parameter order is incorrect cells command has to come before any of the other parameters:

scsnvmisc cells --skip-mt -o /home/jhmoon/data/dami/sample /home/jhmoon/data/dami/sample/summary.h5
earn97 commented 2 years ago

Thank you for you comments. Now it works perfectly.

I'm sorry but I have another question. I don't understand what is the input of scsnvmisc merge.

scsnvmisc merge -n scsnv -n cellranger --vcf <snvs>.vcf -o sample/merged scsnv/pileup cellranger/pileup

What is <snvs>.vcf and cellranger/pileup? And I have pileup files in the sample directory, not in scsnv directory. Please let me know what is the input.

GWW commented 2 years ago

The merge command is for benchmarking where you have SNV calls from another tools. The scsnvmisc annotate command is the one that will call SNVs from a pileup file.