[miso-users] Trouble indexing hg19 alt_events

[Elizabeth Theusch]

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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