[miso-users] cannot import name defaultdict error about MISO

[Huajing Teng]

Dear Dr,
I have installed MISO. When module_availability.py was used, all modules are available. However when i run test_miso.py, i got error:cannot import name defaultdict
  [tenghuajing at master misopy]$ python2.6 test_miso.py
Testing conversion of SAM to BAM...
Executing: python /home/share1/huajingteng/soft/misopy-0.4.3/misopy/sam_to_bam.py --convert /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-data/sam-data/c2c12.Atp2b1.sam /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-output/sam-output
Converting SAM to BAM...
  - Executing: samtools view -Sbh /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-data/sam-data/c2c12.Atp2b1.sam  > /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.bam
[samopen] SAM header is present: 35 sequences.
Sorting BAM file...
  - Executing: samtools sort /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.bam /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.sorted
Indexing BAM...
  - Executing: samtools index /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
Conversion took 0.02 minutes.
.Testing gene-level Psi...
Testing GFF indexing of: /home/share1/huajingteng/soft/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: python /home/share1/huajingteng/soft/misopy-0.4.3/misopy/index_gff.py --index /home/share1/huajingteng/soft/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /home/share1/huajingteng/soft/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1/indexed
Traceback (most recent call last):
  File "/home/share1/huajingteng/soft/misopy-0.4.3/misopy/index_gff.py", line 11, in ?
    from collections import defaultdict
ImportError: cannot import name defaultdict
Executing: python /home/share1/huajingteng/soft/misopy-0.4.3/misopy/run_events_analysis.py  --compute-genes-psi /home/share1/huajingteng/soft/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1/indexed /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /home/share1/huajingteng/soft/misopy-0.4.3/misopy/test-output/gene-psi-output --read-len 35 
Traceback (most recent call last):
  File "/home/share1/huajingteng/soft/misopy-0.4.3/misopy/run_events_analysis.py", line 9, in ?
    from collections import defaultdict
ImportError: cannot import name defaultdict
.
----------------------------------------------------------------------
Ran 2 tests in 3.596s

OK

I wonder whether you can give me some suggestion. Thank you very much.

 				
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Huajing Teng