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Some complex participants not correctly summarized in ComplexTab #195

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rebki opened this issue Mar 18, 2020 · 3 comments
Open

Some complex participants not correctly summarized in ComplexTab #195

rebki opened this issue Mar 18, 2020 · 3 comments

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@rebki
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rebki commented Mar 18, 2020

I'm submitting a ... (check one with "x")

[x] bug report => search existing issues for a similar problems/requests
[ ] feature request
[ ] support request => Please do not submit support request here, instead see: http://www.ebi.ac.uk/support/intact

Current behaviour

For some of the complexes in the downloaded ComplexTab file, the molecules contained in the complex are listed individually with stoichiometry (1), although there are more than one of that type of molecule. For example, the following complex consists of one subcomplex and 4 homodimers, which are listed individually.

$ grep "^CPX-1920" homo_sapiens.tsv | cut -f 1-5
CPX-1920	Complement C1 complex	-	9606	P09871-PRO_0000027587(1)|P00736-PRO_0000027578(1)|P00736-PRO_0000027578(1)|P09871-PRO_0000027587(1)|CPX-1919(1)|P09871-PRO_0000027588(1)|P09871-PRO_0000027588(1)|P00736-PRO_0000027579(1)|P00736-PRO_0000027579(1)

In the browser view, these complex participants are summarized correctly though (https://www.ebi.ac.uk/complexportal/complex/CPX-1920).

Expected behaviour

ComplexTab should list complex participants with the correct stoichiometry, as also shown on the web page:

CPX-1920	Complement C1 complex	-	9606	P09871-PRO_0000027587(2)|P00736-PRO_0000027578(2)|CPX-1919(1)|P09871-PRO_0000027588(2)|P00736-PRO_0000027579(2)

What is the motivation / use case for changing the behaviour?

This is just a minor bug, but it makes it more difficult to see the actual stoichiometry of the complex, especially in case of the long PRO IDs. Also, the current behaviour is an inconsistency within the ComplexTab file as well as between the file and the browser representation.

Please tell us about your environment:

Ubuntu 16.04 with Firefox

Just a few guidelines for how to write effective and good GitHub issues: HOW WE WRITE GITHUB ISSUES
@bmeldal
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bmeldal commented Mar 18, 2020

Thank you for your feedback, Rebecca.

@noedelta is this already on our list to look at?

@bmeldal
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bmeldal commented Mar 20, 2020

Rebecca, I just had time to check: this is a known issue (@noedelta -> Jira CP-207) and is on our to-do-list.

For the time being, I'm afraid, you will need to collapse the stoichiometry at your end.

The stoichiometry is expanded by default for complex that have participants with specific binding features. For all other complexes the stoichiometry is collapsed by default anyway.

Please do not hesitate to send us more feedback or suggestions.

@rebki
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rebki commented Mar 20, 2020

Ok, no problem, thank you for checking. And nice to know where the differing behaviour comes from.

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