Closed hansenp closed 2 years ago
I also got this error. Strange, because CDR1 appear to be right here: https://github.com/monarch-initiative/SLDBGen/blob/master/data/steckel-2012-KRAS.tsv#L311
Ah, the real issue is probably that CDR1 isn't in the downloaded protein-coding_gene.txt
.
There's a similar problem in Sun 2019 with C7orf26 (see Sun-TableS9.txt)
Removing the missing gene symbols from steckel-2012-KRAS.tsv and Sun-Table29.txt allows the process to complete.
Strange I am not getting this error https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1798
@caufieldjh I am now adding some new publications but would like to finalize this dataset next week. Is this error still happening on your side?
I appear to still be experiencing this issue on a fresh install - running python parse_human_SLI.py
gets me a virtually identical error to what's seen above:
$ python parse_human_SLI.py
[INFO] Will download protein-coding_gene.txt
100% [..........................................................................] 9293239 / 9293239[INFO] Astsaturov et al 2010: 60 positive and 0 negative entries
[INFO] Baldwin et al 2010: 2 positive and 0 negative entries
[INFO] Blomen et al 2015: 133 positive and 0 negative entries
[INFO] Bommi et al 2008: 178 positive and 0 negative entries
[INFO] Brough et al 2018: 182 positive and 0 negative entries
[INFO] chakraborty et al 2017: 13 positive and 17 negative entries
[INFO] chin 2020: 3 positive and 0 negative entries
[INFO] Dai et al 2013: 8 positive and 0 negative entries
[INFO] Etemadmoghadam et al 2013: 24 positive and 0 negative entries
[INFO] Han et al 2017: 30 positive and 0 negative entries
[INFO] Josse et al 2014: 7 positive and 1424 negative entries
[INFO] Kang et al 2015: 8 positive and 0 negative entries
[INFO] Kessler et al 2012: 383 positive and 0 negative entries
[INFO] Kim et al 2011: 15 positive and 0 negative entries
[INFO] Krastev et al 2011: 3 positive and 0 negative entries
[INFO] Lord et al 2008: 9 positive and 124 negative entries
[INFO] Luo et al 2009: 81 positive and 0 negative entries
[INFO] Manually entered single-SLI studies (part zero): 51 positive and 6 negative entries
[INFO] Manually entered single-SLI studies (part one): 70 positive and 0 negative entries
[INFO] Manually entered (3): 6 positive and 0 negative entries
[INFO] Martin et al 2010/2011: 18 positive and 2 negative entries
[INFO] Mengwasser et al 2019: 5 positive and 0 negative entries
[INFO] Mohni et al 2014: 41 positive and 307 negative entries
[INFO] Mondal et al 2019: 6 positive and 4 negative entries
[INFO] Oser et al 2019: 103 positive and 0 negative entries
[INFO] Patidar 2020: 13 positive and 3 negative entries
[INFO] Schick et al 2019 n=3 SL interactions
[INFO] Schick et al 2019: 3 positive and 0 negative entries
[INFO] Shen et al 2015 : 7 positive and 104 negative entries
[INFO] Shen et al 2017: 168 positive and 10 negative entries
[INFO] Srivas et al 2016: 180 positive and 0 negative entries
Traceback (most recent call last):
File "parse_human_SLI.py", line 146, in <module>
steckel2012_list = steckel2012.parse()
File "/home/harry/SLDBGen/idg2sl/parsers/steckel_2012_parser.py", line 75, in parse
raise ValueError("Could not find id for gene %s in Steckel 2012" % geneB_sym)
ValueError: Could not find id for gene CDR1 in Steckel 2012
I experience the same error on the develop
branch.
@caufieldjh
I found out that the error is coming because the script downloads the protein-coding_gene.txt
file from HGNC, and on my machine I was still using an old version. In the meantime, two genes have changed symbols or definitions. I could reproduce the above error and was able to fix it, and think things should be OK now. Please close if you can run the script without error.
Great, it works without issue now:
We got 12391 interactions including 2685 synthetic lethal interactions
(I don't have the permissions to close this issue, unfortunately)
Thanks!
I checked out SLDBGen and was able to successfully complete all setup commands in the
README.md
. There were no errors in the tests either.But when I try to generate the list with the SL pairs, I get the following error message: