[miso-users] Syntax error with MISO

[Yarden Katz]

Dear Katerina,

That's odd, I do not get this error on my end.  Could you please let me know what version you're using?  Are you using the latest stable release or the version available on GitHub? 

Also, just to confirm, it looks like you're using Python 2.7, is that right?

Thanks.  Best, --Yarden




On Mar 5, 2013, at 9:35 PM, Katerina Bendak wrote:

> Dear Yarden,
>  
> I have only just started using MISO and am not very experienced with bioinformatics. I have mapped my RNA-seq data with TOPHAT and am currently trying to detect differentially spliced exons with MISO. The program unfortunately seems to run into a syntax error. I pasted everything below. Maybe you have an idea what could be going wrong?
>  
> katschi at rupertbear all_samples_complete]$ run_events_analysis.py --compute-genes-psi hg19_indexed_SE_events/ 10L_thout/10L_accepted_hits.sorted.bam --output-dir 10L_thout/10L_exons --read-len 50 --paired-end 120 23 MISO (Mixture of Isoforms model) Probabilistic analysis of RNA-Seq data to detect differential isoforms Use --help argument to view options.
>  
> Loading settings from: /programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt
> Computing gene-level Psi for genes...
>   - GFF index: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events
>   - BAM: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam
>   - Read length: 50
>   - Output directory: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons
> Mapping genes to their indexed GFF representation, using /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr6
>   - Loading 1762 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr7
>   - Loading 2059 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr5
>   - Loading 1595 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr19
>   - Loading 2343 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr1
>   - Loading 4035 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr4
>   - Loading 1466 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr8
>   - Loading 1386 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr2
>   - Loading 2781 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chrY
>   - Loading 45 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr18
>   - Loading 574 genes
> Skipping: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/genes_to_filenames.shelve
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr15
>   - Loading 1366 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr10
>   - Loading 1774 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chrX
>   - Loading 1146 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr11
>   - Loading 2287 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr16
>   - Loading 1709 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr12
>   - Loading 2301 genes
> Skipping: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/compressed_ids_to_genes.shelve
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr13
>   - Loading 715 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr17
>   - Loading 2146 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr21
>   - Loading 438 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr14
>   - Loading 1280 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr3
>   - Loading 2397 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr9
>   - Loading 1524 genes
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr22
>   - Loading 1002 genes
> Skipping: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/genes.gff
> Loading indexed gene filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr20
>   - Loading 1101 genes
> Preparing to run 4 batches of jobs...
> Running batch of 9808 genes..
>   - Executing: python /programs/apps/miso/bin/run_miso.py --compute-genes-from-file "/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-0_genes.txt" /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons --read-len 50  --paired-end 120.0 23.0 --settings-filename /programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt
>   - Submitted thread batch-0
> Running batch of 9808 genes..
>   - Executing: python /programs/apps/miso/bin/run_miso.py --compute-genes-from-file "/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-1_genes.txt" /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons --read-len 50  --paired-end 120.0 23.0 --settings-filename /programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt
>   - Submitted thread batch-1
> Running batch of 9808 genes..
>   - Executing: python /programs/apps/miso/bin/run_miso.py --compute-genes-from-file "/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-2_genes.txt" /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons --read-len 50  --paired-end 120.0 23.0 --settings-filename /programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt
>   - Submitted thread batch-2
> Running batch of 9808 genes..
>   - Executing: python /programs/apps/miso/bin/run_miso.py --compute-genes-from-file "/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-3_genes.txt" /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons --read-len 50  --paired-end 120.0 23.0 --settings-filename /programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt
>   - Submitted thread batch-3
> Waiting on 4 threads...
>   File "/programs/apps/miso/bin/run_miso.py", line 238
>     with open(genes_filename) as genes_in:
>             ^
> SyntaxError: invalid syntax
>   File "/programs/apps/miso/bin/run_miso.py", line 238
>     with open(genes_filename) as genes_in:
>             ^
> SyntaxError: invalid syntax
> WARNING: Thread batch-0 might have failed...
>   File "/programs/apps/miso/bin/run_miso.py", line 238
>     with open(genes_filename) as genes_in:
>             ^
> SyntaxError: invalid syntax
>   File "/programs/apps/miso/bin/run_miso.py", line 238
>     with open(genes_filename) as genes_in:
>             ^
> SyntaxError: invalid syntax
> WARNING: Thread batch-1 might have failed...
> WARNING: Thread batch-2 might have failed...
> WARNING: Thread batch-3 might have failed...
>   - Threads completed in 0.00 hours.
>  
> Kind regards,
> Katerina
>  
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