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thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
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tidy to HZAR missing POP_ID column issues #151

Closed emilyostrow closed 1 year ago

emilyostrow commented 2 years ago

Hi Thierry,

I am ultimately trying to convert a VCF to an HZAR format. I have imported the VCF successfully, but I am having issues getting radiator to export the tidy dataset to the HZAR format. The problem is surrounding a missing POP_ID column, but I am not sure at which point I am supposed to add it. I tried doing the write_hzar function directly from creating the tidyVCF object and after creating a dummy POP_ID column and I got different errors for each.

For the following code, the error was: Calibrating REF/ALT alleles... Error in write_hzar():
0s! Populations in distances file doesn't match populations in input file Run rlang::last_error() to see where the error occurred. Warning messages: 1: Unknown or uninitialised column: POP_ID. 2: Unknown or uninitialised column: POP_ID. 

tidyVCF <- tidy_vcf(data="OptimalFiltered.vcf")
hzar_filtered <- write_hzar(
  tidyVCF,
  distances = "distances2.txt",
  filename = NULL,
  parallel.core = parallel::detectCores() - 1
)

For the code with distances =NULL, the error was: Calibrating REF/ALT alleles... Error in distinct_prepare(): ! distinct() must use existing variables. x POP_ID not found in .data. Run rlang::last_error() to see where the error occurred. Warning message: Unknown or uninitialised column: POP_ID. 

hzar_filtered <- write_hzar(
  tidyVCF,
  distances = NULL,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1
)

For the following code with the dummy POP_ID column, the error was: Calibrating REF/ALT alleles... Error in stop_vctrs(): ! Names must be unique. x These names are duplicated:

I am clearly doing something wrong here surrounding the POP_ID column, but I am not sure how to fix it. Any advice would be greatly appreciated. Thank you.

Session Info: setting value version R version 4.1.1 (2021-08-10) os macOS Big Sur 11.2.1 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Chicago date 2022-02-02 rstudio 1.4.1717 Juliet Rose (desktop) pandoc NA

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[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library

thierrygosselin commented 1 year ago

re-open the issue following guidelines if this is still relevant with latest release. Otherwise, you can use stacks populations module to get a HZAR file from a vcf.