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

[Gabriel Otte]

Hi.  I have the same error when running my test.  Please advise.

Best,

Gabe
On Jul 13, 2012, at 7:48 AM, Huajing Teng wrote:

> 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.
> 
> 				
> --------------
> Huajing Teng
> 
> 
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