MakeDb.py, KeyError: 'subject seq'

[Michael Swift]

Hi there,

Thanks for writing this software.

I'm having trouble running the script MakeDb.py on the example dataset.

I installed change-o using pip and other parts of the package seem to work fine for me. However MakeDb.py on the test data set throws me an error, when I use the command shown on the readthedocs page.

I've attached the commands I've tried and the errors I am getting.

Many thanks

[Jason Vander Heiden]

Greetings @mswift2,

Thanks for reporting this!

It looks like the example IgBLAST file wasn't generated correctly and was missing the required subject seq column from the # Hit table section. I remade the IgBLAST output and uploaded a new Changeo_Example.tar.gz file.

It now works locally for me via:

cd Changeo_Example
MakeDb.py igblast -i S43_atleast-2.fmt7 -s S43_atleast-2.fasta -r IMGT_Human_IGHV.fasta IMGT_Human_IGHD.fasta IMGT_Human_IGHJ.fasta --regions --scores

Let me know if it gives you anymore trouble.

[Michael Swift]

Thanks that seems to run for me now! I get 7 failed databases entries is that behavior expected?

Also FYI there's a minor issue for me with the Read the Docs site. When I use the search function the links in the results are broken.

Thanks, Michael

[Jason Vander Heiden]

Yeah, a small number of failures is normal. Typically due to truncated sequences missing the CDR3 and/or J.

If you add the --partial argument to MakeDb, which allows incomplete sequences to pass the filters, then you should get zero sequences that fail.

Regarding the ReadTheDocs site, can you give me an example search that fails? I'm not having any luck reproducing the problem.

Though, I did make a couple changes to the docs site settings that might help? Let me know.

[Michael Swift]

Okay cool thanks!

an example of the read the docs site is that for me I type in "fail" in the search bar and it returns results. But when I click on those results I get a result that the webpage doesn't exist.

Search page: https://changeo.readthedocs.io/en/version-0.3.5---imgt-and-igblast-fixes/search.html?q=fail&check_keywords=yes&area=default

Clicking on the first link: https://changeo.readthedocs.io/en/version-0.3.5---imgt-and-igblast-fixes/tools/MakeDb.rst.html?highlight=fail#cmdoption-makedb-imgt-failed

yields this for me:

[Jason Vander Heiden]

Thanks, @mswift2. That's weird. I see the error with the v0.3.5 docs (and v0.3.4), but it doesn't occur in the docs for v0.3.6 through v0.3.12.

I tried rebuilding the docs for v0.3.5, but it didn't fix.

The code that builds the docs is locked into the same version as the code for the package, so I can't really fix the v0.3.5 docs without making a new version if it's a problem with the docs code (which it probably is).

I'd say just use the v0.3.6 docs if you need to use v0.3.5. The difference between those versions is minor. (If you don't need to use v0.3.5, then I'd upgrade to v0.3.12 - there are some bug fixes that matter.)

[Michael Swift]

Huh interesting, didn't realize I was using an older version. The v0.3.6 link didn't reproduce my error i.e. it works. Thanks!

[Jason Vander Heiden]

All is well.