[miso-users] indexing GFF

[Daniel Sobral]

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