KeyError: 'V Frame shift'

[Camille Brewer]

Hi,

I am hoping to use changeo to analyze some bcr data from 10X, but I am having trouble.

When I use MakeDb.py I get the error KeyError: 'V Frame shift', and I am not sure what I am doing wrong.

Any help would be greatly appreciated!

Camille

python3 MakeDb.py igblast -i /labs/wrobins/RCamille/Ig_analysis/ChangeO/C09_Rectum2/filtered_contig_igblast.fmt7 -s /labs/wrobins/RCamille/10X/cellranger-4.0.0/C09_Rectum_bcr2/outs/filtered_contig.fasta -r /labs/wrobins/RCamille/Ig_analysis/germlines/imgt/human/vdj/imgt_human_IG*.fasta --10x /labs/wrobins/RCamille/10X/cellranger-4.0.0/C09_Rectum_bcr2/outs/filtered_contig_annotations.csv --extended START> MakeDB COMMAND> igblastALIGNER_FILE> filtered_contig_igblast.fmt7 SEQ_FILE> filtered_contig.fasta ASIS_ID> False ASIS_CALLS> False PARTIAL> False EXTENDED> TruePROGRESS> 21:43:51 |Done | 0.0 minPROGRESS> 21:43:51 | | 0% ( 0) 0.0 minTraceback (most recent call last): File "MakeDb.py", line 885, in <module> args.func(**args_dict) File "MakeDb.py", line 538, in parseIgBLAST regions=regions, writer=writer, out_file=out_file, out_args=out_args) File "MakeDb.py", line 271, in writeDb for i, record in enumerate(records, start=1): File "MakeDb.py", line 535, in <genexpr> germ_iter = (addGermline(x, references, amino_acid=amino_acid) for x in parse_iter) File "/oak/stanford/scg/lab_wrobins/RCamille/Ig_analysis/ChangeO/changeo/IO.py", line 1521, in __next__ sections = self.parseBlock(block) File "/oak/stanford/scg/lab_wrobins/RCamille/Ig_analysis/ChangeO/changeo/IO.py", line 1409, in parseBlock chunk_dict = {k: f(chunk) for k, (v, f) in chunk_map.items() if chunk[0].startswith(v)} File "/oak/stanford/scg/lab_wrobins/RCamille/Ig_analysis/ChangeO/changeo/IO.py", line 1409, in <dictcomp> chunk_dict = {k: f(chunk) for k, (v, f) in chunk_map.items() if chunk[0].startswith(v)} File "/oak/stanford/scg/lab_wrobins/RCamille/Ig_analysis/ChangeO/changeo/IO.py", line 951, in _parseSummaryChunk columns = [summary_map[x.strip()] for x in f.split(',')] File "/oak/stanford/scg/lab_wrobins/RCamille/Ig_analysis/ChangeO/changeo/IO.py", line 951, in <listcomp> columns = [summary_map[x.strip()] for x in f.split(',')]KeyError: 'V Frame shift'

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[Jason Vander Heiden]

Greetings @Camille Brewer ,

Thanks for the bug report. V Frame shift is a field that igblast just recently added in v1.17.0 (October release), so this is probably a changeo bug caused by not parsing the new field correctly. Though, I thought the newest version of change (v1.0.1) passed our tests against iblast v1.17.0. I will run some tests.

Which version of changeo are you using? (Reported by MakeDb.py --version.)

[Camille Brewer]

Hi Jason,

Thanks for you reply! The verison I am using is 1.0.1 2020.10.13

Should I try an older MakeDb?

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[Jason Vander Heiden]

Thanks. No, I don’t think an older version of changeo will work. An older version of igblast should, but this looks like a bug we need to fix. We’ll figure it out and get back to you soon.

[Jason Vander Heiden]

This should now be fixed in the development version of changeo (the tip of master). You can install it via:

pip3 install git+https://bitbucket.org/kleinstein/changeo@master --user

(Only specify the --user flag if that’s how you previously installed changeo.)

If you’re using the docker container, the build for that is running. The fix should be in the immcantation/suite:devel image in a couple hours - once the build finishes. We’ll push out a new official changeo release in the near future. Probably not until next week though.

Please let us know if this doesn’t work and I’ll hammer on it some more.

[Camille Brewer]

Hi Jason,

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Thanks for looking into this – I am still getting the same V-frame error

do I need to change any of my .py files?

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[Jason Vander Heiden]

The .py files should be updated via the pip3 install process. Did the install work? Has your changeo version changed? (You may need to add the --upgrade argument to the pip3 command.)

[Camille Brewer]

Oops- I was still running the old version (sorry!) - It has updated It works! Thanks! I really appreciate your help!

[Jason Vander Heiden]

Great! Glad to hear it. I’ll close this, but let us know if you have any problems.

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[Jason Vander Heiden]

Fixed in 8ac8292.