Update Hotspots to grch38 #59
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...added settings to requests calls to timeout and retry
File was updated by running the script scripts/hotspots/update_hotspots_to_grch38.py
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Genes dropped and genes updated are attached |
| type=str, help="which transcript override source is preferred. Possible values: [mskcc, uniprot, genome_nexus, ensembl]") | ||
| parser.add_argument("--grch37_hotspots_2d_3d_file_name", default="../../data/grch37_ensembl92/export/hotspots_v2_and_3d.txt", | ||
| type=str, help="combined grch37 2D and 3D cancerhotspots data file") | ||
| args = parser.parse_args() |
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FYI - the updated hotspots file in this PR was produced by running this script with the default values for all these arguments ^
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@pieterlukasse Thanks! Is there a place where this would fit in the Makefile? https://github.com/genome-nexus/genome-nexus-importer/blob/master/data/common_input/hotspots/Makefile
We've been trying to use the Makefiles as a way to build all the export/ files. Ideally we can build everything with this command:
https://github.com/genome-nexus/genome-nexus-importer#running
I think that hotspots are separately tho in this Makefile (should prolly be added to the docs how that works at some point):
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@inodb good idea. I've pushed up an extra commit with the changes to the hotspots Makefile, and added a subsection to the README. Please take a look and let me know what you think.
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| ../../grch37_ensembl92/export/hotspots_v2_and_3d.txt: hotspots_v2_and_3d_grch37.txt | ||
| cp $< $@ | ||
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| ../../grch38_ensembl92/export/hotspots_v2_and_3d.txt: hotspots_v2_and_3d_grch37.txt_grch38_ported.txt |
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Do you have new "../../grch38_ensembl92/export/hotspots_v2_and_3d.txt" uploaded in the pull request?
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I did run it. Do you want me to upload it or do you want to run it to test the process? The final result should be identical to the grch38_ensembl95 one, given the Ensembl api the script is using.
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Will copy the file over for now on our end - thanks!
Fixes #58