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JiekaiLab / scTE

MIT License
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args.out <-> outname problem #8

Closed melonheader closed 3 years ago

melonheader commented 3 years ago

Hello, I am PhD student working with single cell data I read your research paper on TE quantification in single-cell data. Very witty!

It prompted me to try out your pipeline, but it crushed with an error soooo close to an end. I looked the source code on git hub, and it seems I had found the source of an error.

At the line 155 where the Counterexpression function is called, for a filename argument it takes args.out, which is an output path specified by the user. Throughout the pipeline the outname ( basename of args.out ) is used, and all of the temporary files are saved to the working directory using the outname as a prefix for tmp folder.

Thus, when Counterexpression is called with args.out, it looks for temporary files following incorrect paths; from base.py:

def Countexpression(filename, allelement, genenumber, cellnumber, hdf5):
    gene_seen = allelement

    whitelist={}
    o = gzip.open('%s_scTEtmp/o4/%s.bed.gz'%(filename, filename), 'rt')

Temporarily changing args.out to outname solved this problem for me and pipeline ran smoothly. All the output files were saved to the directory from where the original script were run.