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broadinstitute / gtex-pipeline

GTEx & TOPMed data production and analysis pipelines
BSD 3-Clause "New" or "Revised" License
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Syntax error #85

Closed qicaibiology closed 1 week ago

qicaibiology commented 1 year ago

I was trying to run the command using: python3 collapse_annotation.py gencode.vM25.annotation.gtf gencode.vM25.genes.gtf

I used anacondas environment to use python3, and use gencode.vM25.annotation.gtf as input and output is supposed to be gencode.vM25.genes.gtf. I got the following error and I don't know what to do:

File "/gpfs/gibbs/project/sestan/cq39/PMID_30678683/combined_bams/collapse_annotation.py", line 76

gtex-pipeline/gene_model/collapse_annotation.py at master · broadinstitute/gtex-pipeline · GitHub 
                                                                 ^

SyntaxError: invalid character '·' (U+00B7)

Thanks

francois-a commented 1 year ago

The script runs fine on this GTF (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz), this must be an issue with your environment.