Comments (6)
Hello,
The issue should be fixed now. Please do a git pull to update the vcf2bgc.py script and try running it again. Let me know if you are still having issues with the script.
The problem was that I had accidentally turned the linkage model on by default, but it should have to be toggled on to use it. Because the example file as well as your own data file had chromosomes with only one site, the script was dividing by zero when it tried to normalize the position maps between 0 and 1.
I turned the option to generate linkage maps off by default now, and I added error handling for if the linkage map file has chromosomes with only one position.
Thanks,
-Bradley
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Hi Irene,
It looks like the list.clear() which is throwing the error was added in Python 3.3, so I'm guessing you are using an older version of Python than 3.3. I just added a fix that should work with Python3 versions older than 3.3, could you give that a try?
Thanks,
Tyler
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Hello,
Thank you for your interest in ClineHelpR. I will look into what may be happening with the vcf2bgc.py script this evening. Sorry for the issue.
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You're very welcome. Glad to see it's working now. Thanks for your interest in ClineHelpR.
-Bradley
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Related Issues (17)
- Add vcf2bgc script
- pafscaff HOT 6
- Hybrid Index HOT 1
- Error with parsing alleles depth HOT 7
- Error HOT 9
- get_bgc_outliers error HOT 15
- Rename snps$crazy.a and snps$crazy.b to something more intuitive
- Rebuild docker image with updates to vcf2bgc.py HOT 1
- Fix run_bgc.sh estpost LnL file naming HOT 1
- run bgc error in docker HOT 3
- ClineHelpR R package conda install? HOT 1
- jinja2 HOT 2
- R function: combine_bgc_output HOT 2
- GSL error. HOT 2
- phiPlot visualization issue HOT 1
- Assessing the convergence of runs HOT 2
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