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Error when running iSAFE using haps converted using plink2 #19
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Hi, The current implementation of iSAFE is unable to process the entire genome. Many selection scan tools, such as those listed at slescan, are designed for this purpose. However, I have addressed a similar question in #6, which details how to use iSAFE for this purpose. A similar approach was used in Colomer-Vilaplana et al. 2022. Could you please share a small example of your input along with the error so that I can replicate it? Best, |
The error is occurring because the POS variable contains string values instead of numeric values, and the subtraction operation is not supported between strings. Please ensure all POS values are numeric. |
Can I run iSAFE using a vcf file on the entire chromosome?
Second, I tried to run iSafe on the haps file after converting the vcf containing phased data to haps by plink2.
But I ended up getting an error, as shown below.
File "/home/miniconda3/envs/iSafe/bin/isafe", line 10, in
sys.exit(run())
^^^^^
File "/home/miniconda3/envs/iSafe/lib/python3.12/site-packages/isafe/isafe.py", line 185, in run
total_window_size = POS.max() - POS.min()
~~~~~~~~~~^~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'str' and 'str
What could be the reason for this error?
Also, I want to scan selection loci using iSAFE on the entire chromosome without specifying a specific region. How can I use iSAFE for this purpose?
my input file looks like this
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