Need help with "Get Pathways" tool

Question: Need help with "Get Pathways" tool

3.9 years ago by

United Kingdom

Hi,

i am trying to get the KEGG AND GO pathways fro a given ensemble of transcripts with no success and I cannot figure out the nature of the error as my input file has been uploaded under the tabular format. I compare this set with the last Human catalogue (2013).

ENSG00000124731
ENSG00000163013
ENSG00000064687
ENSG00000180424
ENSG00000112033
ENSG00000135249
ENSG00000116030
ENSG00000175170
ENSG00000110841
ENSG00000214929
ENSG00000181690

this is my stderr :

Traceback (most recent call last):
  File "/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/884ccb07885b/genome_diversity/rtrnKEGGpthwfENSEMBLTc.py", line 77, in <module>
    main()
  File "/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/884ccb07885b/genome_diversity/rtrnKEGGpthwfENSEMBLTc.py", line 43, in main
    crDB=[x.split() for x in open(loc_file).read().splitlines() if x.split()[0]==species][0]
IndexError: list index out of range

Tool name: Get Pathways
Tool version: 1.0.0
Tool ID: toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_new_oscar/1.0.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/miller-lab/genome_diversity

software error get-pathways • 1.0k views

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modified 21 months ago by pabrennan • 0 • written 3.9 years ago by andr.agostinelli • 0

3.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The immediate issue is that the tool is expecting a two-column input dataset. In your case, the build name is missing. Here is the help quote from the "Get Pathways" tool form:

Dataset formats

The input and output datasets are in tabular format. The input dataset must have a column with an ENSEMBL transcript ID and have the database/build set. Even though positions are not needed the correct database/build must be given to look up the pathways. The output dataset will have added columns for the pathway.

There is also a content issue, as these are gene identifiers, not transcript identifiers. For transcripts associated with this gene, I just searched at Ensembl, here is the page:
http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000124731;r=6:41267926-41286719;t=ENST00000591620;redirect=no

Hopefully by making the necessary input corrections, things will work out, but please let us know if not. Jen, Galaxy team

ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

21 months ago by

pabrennan • 0

pabrennan • 0 wrote:

Hello,

My "Get Pathways" tool does not work as well. I get the same error message as the top guy, but I have mouse Ensembl transcripts, and I set the database/build to "Mouse Dec. 2011 (mm10)". My input is tabular with 16 columns and I have one column with the Ensembl transcript IDs. Is there anything else I can try to get the KEGG pathways?

Thanks, Paul

ADD COMMENT • link written 21 months ago by pabrennan • 0

Hi Paul, This is an older tool with no plans for an update. The list of genomes that will work (using the cached legacy reference data) are hg19, canFam2, and bosTau4. Unfortunately, data from mouse are not accepted. Other tools access KEGG pathways (for example, GEMINI), yet this may not meet your use case. A stand-alone tool for just this function (any list of Ensembl IDs -> KEGG pathway) does not exist yet. Jen, Galaxy team

ADD REPLY • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

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