[miso-users] Trouble indexing hg19 alt_events

[Yarden Katz]

Hi,

Can you try it again, but prior to the call do:

$ mkdir /home/mdata/Beth/IndexSeqFiles/ForMISO/hg19/indexed/

and try again?  I will commit a fix to this issue.  When I put it into a directory that exists, I cannot reproduce your error:

$ python index_gff.py --index SE.hg19.gff3 ~/test-index/
Indexing GFF...
  - GFF: /home/yarden/sugarman/gff-events/hg19/SE.hg19.gff3
  - Outputting to: /home/yarden/test-index
..warning snipped...
Through 0 genes...
Through 5000 genes...
Through 10000 genes...
Through 15000 genes...
Through 20000 genes...
Through 25000 genes...
Through 30000 genes...
Through 35000 genes...
Loaded 39232 genes
  - Loading of genes from GFF took 32.41 seconds
Making directory: /home/yarden/test-index/chrY
  - Chromosome serialization took 3.99 seconds
Making directory: /home/yarden/test-index/chrX
...remaining output for other chromosomes...


Let me know if that works.

Thanks, --Yarden 


On Dec 23, 2011, at 4:38 PM, Elizabeth Theusch wrote:

> Hello,
> I am trying to test out the latest version of MISO, but I haven’t been able to get past the indexing (pickling) step.  Am I doing something wrong?  (See below)  I know that the pickled versions were taken out of the download, but is there any way I can try them out to see if they work for me?  I would really like to test this before the new year.
> Thanks, and happy holidays,
> Beth Theusch
>  
> python index_gff.py --index /home/mdata/Beth/IndexSeqFiles/ForMISO/hg19/SE.hg19.gff3 /home/mdata/Beth/IndexSeqFiles/ForMISO/hg19/indexed/
> Indexing GFF...
>   - GFF: /home/mdata/Beth/IndexSeqFiles/ForMISO/hg19/SE.hg19.gff3
>   - Outputting to: /home/mdata/Beth/IndexSeqFiles/ForMISO/hg19/indexed
> WARNING: Swapping start and end fields, which must satisfy start <= end:
> GFF('chr13', 'SE', 'gene', 114541163, 114549499, None, '+', None, {'ID': ['chr13:114549499:114551209:+ at chr13:114542700:114542822:+ at chr13:114541041:114541163:+'], 'Name': ['chr13:114549499:114551209:+ at chr13:114542700:114542822:+ at chr13:114541041:114541163:+']})
> .
> . (more warnings here, but I don’t think they are relevant to this problem)
> .
> Through 0 genes...
> Through 5000 genes...
> Through 10000 genes...
> Through 15000 genes...
> Through 20000 genes...
> Through 25000 genes...
> Through 30000 genes...
> Through 35000 genes...
> Loaded 39232 genes
>   - Loading of genes from GFF took 23.51 seconds
> Making directory: /home/mdata/Beth/IndexSeqFiles/ForMISO/hg19/indexed/chrY
> Traceback (most recent call last):
>   File "index_gff.py", line 120, in <module>
>     main()
>   File "index_gff.py", line 116, in main
>     index_gff(gff_filename, output_dir)
>   File "index_gff.py", line 97, in index_gff
>     serialize_genes(gff_genes, output_dir)
>   File "index_gff.py", line 56, in serialize_genes
>     gene_filename)
>   File "/home/btheusch/bin/MISO/pickle_utils.py", line 16, in write_pickled_file
>     pickled_file = file(pickled_filename, 'w')
> IOError: [Errno 20] Not a directory: '/home/mdata/Beth/IndexSeqFiles/ForMISO/hg19/indexed/chrY/chrY:21749096:21749393:+ at chrY:21750256:21750297:+ at chrY:21751407:21751498:+.pickle'
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