[miso-users] Syntax error with MISO

Thu Mar 7 00:22:27 EST 2013

Hi Yarden

Thanks for your quick response!! I am using the latest stable release
(misopy 0.4.7) and python 2.7. I have no idea what could cause this error.
If you have any idea, I would be very grateful if you could help!

Kind regards,
Katerina

-----Original Message-----
From: Yarden Katz [mailto:yardenny at gmail.com] On Behalf Of Yarden Katz
Sent: Wednesday, 6 March 2013 15:28
To: Katerina Bendak
Cc: miso-users at mit.edu
Subject: Re: [miso-users] Syntax error with MISO

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_a
ccepted_hits.sorted.bam
>   - Read length: 50
>   - Output directory:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons
> 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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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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