[miso-users] new release of MISO

[Roberta Carriero]

I downloaded and used the new release of MISO (0.5.2). I obtained the  
following error:



[carriero at node01 misopy]$ python miso.py  
--settings-filename=/data/misopy-0.5.2/misopy/settings/miso_settings.txt --run  
/data/home/carriero/miso/indexed_SE_events  
/data/home/carriero/miso/risultati/7A3_1/TOPHAT_OUT/accepted_hits1.bam  
--output-dir /data/home/carriero/02042014/Miso7A3_1/ --read-len 100  
--paired-end 239.2 56.5 --event-type=SE
MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data for detecting differential isoforms
Use --help argument to view options.

Using MISO settings file: /data/misopy-0.5.2/misopy/settings/miso_settings.txt
Computing Psi values...
   - GFF index: /data/home/carriero/miso/indexed_SE_events
   - BAM:  
/data/home/carriero/miso/risultati/7A3_1/TOPHAT_OUT/accepted_hits1.bam
   - Read length: 100
   - Output directory: /data/home/carriero/02042014/Miso7A3_1
Checking your GFF annotation and BAM for mismatches...
Checking if BAM has mixed read lengths...
Found reads of length 100 in BAM.
Mapping genes to their indexed GFF representation, using  
/data/home/carriero/miso/indexed_SE_events
Searching for  
/data/home/carriero/miso/indexed_SE_events/genes_to_filenames.shelve..
   - Found shelved file.
Traceback (most recent call last):
   File "miso.py", line 579, in <module>
     main()
   File "miso.py", line 549, in main
     wait_on_jobs=wait_on_jobs)
   File "miso.py", line 388, in compute_all_genes_psi
     wait_on_jobs=wait_on_jobs)
   File "miso.py", line 106, in __init__
     gff_utils.get_gene_ids_to_gff_index(gff_dir)
   File  
"/data/python27/lib/python2.7/site-packages/misopy/gff_utils.py", line  
99, in get_gene_ids_to_gff_index
     gene_ids_to_gff_index = load_shelved_genes_to_fnames(indexed_gff_dir)
   File  
"/data/python27/lib/python2.7/site-packages/misopy/gff_utils.py", line  
83, in load_shelved_genes_to_fnames
     gene_ids_to_gff_index = shelve.open(shelve_fname)
   File "/data/python27/lib/python2.7/shelve.py", line 239, in open
     return DbfilenameShelf(filename, flag, protocol, writeback)
   File "/data/python27/lib/python2.7/shelve.py", line 223, in __init__
     Shelf.__init__(self, anydbm.open(filename, flag), protocol, writeback)
   File "/data/python27/lib/python2.7/anydbm.py", line 84, in open
     mod = __import__(result)
   File "/data/python27/lib/python2.7/dbhash.py", line 7, in <module>
     import bsddb
   File "/data/python27/lib/python2.7/bsddb/__init__.py", line 67, in <module>
     import _bsddb
ImportError: No module named _bsddb


What about it? How could I solve it?
Thanks in advance

Best Regards

Roberta Carriero
PhD student
Institute of Molecular Genetics Pavia (Italy)