[miso-users] indexing GFF

[Yarden Katz]

Hi Daniel,

This error is now fixed, I was adding a new feature that caused this error.  See "fastmiso" branch for corrected version.

best, --Yarden



On Jul 4, 2012, at 9:43 AM, Daniel Sobral wrote:

> Hello,
> 
> I'm trying miso and I'm having difficulties indexing the gff.
> E.g. :
> index_gff.py --index=genome/miso/modENCODE/modENCODE_RI_MISO.gff3
> genome/miso/indexed_RI_events/
> Indexing GFF...
>  - GFF:
> /home/dsobral/data/project_data/rmartinho/genome/miso/modENCODE/modENCODE_RI_MISO.gff3
>  - Outputting to:
> /home/dsobral/data/project_data/rmartinho/genome/miso/indexed_RI_events
> Through 0 genes...
> Through 5000 genes...
> Through 10000 genes...
> Through 15000 genes...
> Through 20000 genes...
> Through 25000 genes...
> Through 30000 genes...
> Loaded 32895 genes
>  - Loading of genes from GFF took 29.68 seconds
> Making directory:
> /home/dsobral/data/project_data/rmartinho/genome/miso/indexed_RI_events/chr2RHet
> Traceback (most recent call last):
>  File
> "/home/dsobral/data/project_data/rmartinho/virtual_env/bin/index_gff.py", line
> 187, in <module>
>    main()
>  File
> "/home/dsobral/data/project_data/rmartinho/virtual_env/bin/index_gff.py", line
> 183, in main
>    compress_id=options.compress_id)
>  File
> "/home/dsobral/data/project_data/rmartinho/virtual_env/bin/index_gff.py", line
> 157, in index_gff
>    compress_id=compress_id)
>  File
> "/home/dsobral/data/project_data/rmartinho/virtual_env/bin/index_gff.py", line
> 107, in serialize_genes
>    gene_filename)
> UnboundLocalError: local variable 'gene_filename' referenced before
> assignment
> 
> 
> Any help welcome,
> Daniel
> 
> _______________________________________________
> miso-users mailing list
> miso-users at mit.edu
> http://mailman.mit.edu/mailman/listinfo/miso-users