multipleFieldSelection.py issue

[luhan125]

Hello,

When I run "python3.5 ~/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py -i quant.sf -k 1 -f 4 -o 2m-1_iso_tpm.txt", the err is: INFO: Reading file: quant.sf INFO: File quant.sf closed. Traceback (most recent call last): File "/home/yaofw/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py", line 91, in aux2 = aux1.pop() IndexError: pop from empty list

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/yaofw/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py", line 129, in print("ERROR: %s" % err) NameError: name 'err' is not defined

And all the steps are: salmon index -t gencode.vM25.transcripts.fa -i gencode.vM25.transcripts_salmon_index

salmon quant -i gencode.vM25.transcripts_salmon_index -l ISF --gcBias -1 2m_R1.fastq -2 2m_R2.fastq -p 10 -o /xtdisk/guocx_group/yaofw/luhan/testis/suppa-salmon/quant/2m-1

cd /xtdisk/guocx_group/yaofw/luhan/testis/suppa-salmon/quant/2m-1 python3.5 ~/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py -i quant.sf -k 1 -f 4 -o 2m-1_iso_tpm.txt

And when I used "Mus_musculus.GRCm38.cds.all.fa" as transcript annotation, the err was same.

Thank you！

[EduEyras]

Hi,

it seems there is a problem with the format in the expression file. Did you check that the format is as expected by SUPPA? Thanks

E.

On Thu, 4 Jun 2020 at 13:32, luhan125 [email protected] wrote:

Hello,

When I run "python3.5 ~/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py -i quant.sf -k 1 -f 4 -o 2m-1_iso_tpm.txt", the err is: INFO: Reading file: quant.sf INFO: File quant.sf closed. Traceback (most recent call last): File "/home/yaofw/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py", line 91, in aux2 = aux1.pop() IndexError: pop from empty list

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/yaofw/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py", line 129, in print("ERROR: %s" % err) NameError: name 'err' is not defined

And all the steps are: salmon index -t gencode.vM25.transcripts.fa -i gencode.vM25.transcripts_salmon_index

salmon quant -i gencode.vM25.transcripts_salmon_index -l ISF --gcBias -1 2m_R1.fastq -2 2m_R2.fastq -p 10 -o /xtdisk/guocx_group/yaofw/luhan/testis/suppa-salmon/quant/2m-1

cd /xtdisk/guocx_group/yaofw/luhan/testis/suppa-salmon/quant/2m-1 python3.5 ~/.local/lib/python3.5/site-packages/SUPPA/multipleFieldSelection.py -i quant.sf -k 1 -f 4 -o 2m-1_iso_tpm.txt

And when I used "Mus_musculus.GRCm38.cds.all.fa" as transcript annotation, the err was same.

Thank you！

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-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

[luhan125]

Hi,

Thank you for your reply! I have checked the expression file, there was no problem, and I plan to use another tool for transcript quantification. But, I have other strange problem, when I run : python3.5 ~/.local/lib/python3.5/site-packages/SUPPA/suppa.py generateEvents -i /asnas/guocx_group/yaofw/reference/mm9/GRCm38/Mus_musculus.GRCm38.85.format.gtf -o 107190A.events -e SE SS MX RI FL -f ioe The err is : usage: suppa.py [-h] {generateEvents,psiPerEvent,psiPerIsoform,diffSplice,clusterEvents,joinFiles} ... suppa.py: error: unrecognized arguments: -f ioe

I am confused why the err was 'unrecognized arguments: -f ioe', when I put the right script.

Han

[EduEyras]

Hi,

Thanks for the email

maybe it's a thing of python 3.5? With 3.4 should be ok

E

On Wed, 10 Jun 2020 at 19:31, luhan125 [email protected] wrote:

Hi,

Thank you for your reply! I have checked the expression file, there was no problem, and I plan to use another tool for transcript quantification. But, I have other strange problem, when I run : python3.5 ~/.local/lib/python3.5/site-packages/SUPPA/suppa.py generateEvents -i /asnas/guocx_group/yaofw/reference/mm9/GRCm38/Mus_musculus.GRCm38.85.format.gtf -o 107190A.events -e SE SS MX RI FL -f ioe The err is : usage: suppa.py [-h]

{generateEvents,psiPerEvent,psiPerIsoform,diffSplice,clusterEvents,joinFiles} ... suppa.py: error: unrecognized arguments: -f ioe

I am confused why the err was 'unrecognized arguments: -f ioe', when I put the right script.

Han

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-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

[jmirazee]

I think you may run into this issue if you are putting each quant.sf file as a space separated list in the command line. In that case, I commented out the lines containing aux1/2: aux1 = inputFile.split("/"), #aux1.pop(), #aux2 = aux1.pop() I then changed the line outputHeader.append(aux2) to outputHeader.append(inputFile). The reason behind this issue is that pop returns the last value of the list, but if you have each quant.sf file as the only entity in the list, pop will cause an error. So, do the above. In addition, err is not defined and I would recommend replacing the except code with except Exception as e: print(e)