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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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Issues when running diff_iso_usage, needs to run identify_annotated_gene.py first? #255

Closed CWYuan08 closed 1 year ago

CWYuan08 commented 1 year ago

Copy and paste the exact command you tried to run diff_iso_usage flair.quantify.counts.tsv sample1_Parent_batch1 sample2_Parent_batch1 diff_isos.txt

How did you install Flair? (We'd prefer it if you used one of the top two because they are the least likely to have package compatibility problems.)

  1. bioconda (e.g. conda create -n flair -c conda-forge -c bioconda flair)

What happened?

Error message: Please run bin/identify_annotated_gene.py first so that isoforms can be grouped by their parent genes

We know it's ugly but we promise it helps us solve problems faster.

But I couldn't find this function...What should I try? Many thanks!

Jeltje commented 1 year ago

Thanks for reporting this. For now you should be able to find the program at ~/.conda/envs/flair/lib/python3<version>/site-packages/flair/identify_annotated_gene.py or you can pull it directly from this repository:

wget https://raw.githubusercontent.com/BrooksLabUCSC/flair/master/src/flair/identify_annotated_gene.py
chmod 775 identify_annotated_gene.py

I will make sure this is fixed in the next release (the current one is 1.7.2).