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spectra from FPbase #92

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carandraug opened this issue Sep 5, 2019 · 2 comments
Open

spectra from FPbase #92

carandraug opened this issue Sep 5, 2019 · 2 comments

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@carandraug
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FPbase has a spectra and data for a bunch of proteins that we don't. We could have a script that downloads and converts it for spekcheck. Shouldn't be much work.
carandraug added a commit to carandraug/SpekCheck that referenced this issue Sep 5, 2019
@carandraug
update-from-fpbase: script to convert FPbase spectra to SPEKcheck (is…
719878b 
…sue MicronOxford#92)

* src/update-from-fpbase.py: new script to convert a file with
  FPbase json spectra data to SPEKcheck format.
* Makefile: rule to download all proteins from FPbase and add them
  to SPEKcheck.
* NEWS: reference new script.
@carandraug
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I now wrote a quick script that does that. Given a file with all the FPbase protein data on json format, converts to SPEKcheck format and saves to a specific file. I also added a makefile rule that downloads said file.

Only two issues:

#. mKOκ protein has issues not sure exactly where. The last character is a kappa and so name is κ but κ is displayed. Not sure exactly where the issue is, but may be on spekcheck.js assuming simpler filenames.

#. the new script is python 3.7 only

@carandraug
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Spoke with Ian about including all the FPbase proteins on the next release. The problem with it is that it brings 244 fluorescent proteins which is a bit too much. Things we can do:

  • mention the script on the README and tell users to download and copy the ones they want
  • download them all, place them in a separate folder, and tell users to copy the ones they want
  • put them all anyway and tell users to remove the ones they don't want

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@carandraug