create_beast2_input_file() ignores tipdates_filename argument #108
Comments
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Thanks for this bug report! I will take a look now ... |
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Note to self: Indeed, creating the BEAST2 input file works perfect: test_that("use", {
expect_true(file.exists(get_beautier_path("babette_issue_108_tipdates.txt")))
expect_true(file.exists(get_beautier_path("babette_issue_108.fasta")))
fasta_filename <- get_beautier_path("babette_issue_108.fasta")
output_filename <- get_beautier_tempfilename()
tipdates_filename <- get_beautier_tempfilename(pattern = "absent_")
create_beast2_input_file(
fasta_filename,
output_filename,
tipdates_filename = tipdates_filename,
clock_model = create_rln_clock_model(),
site_model = create_gtr_site_model(),
mcmc = create_mcmc(),
tree_prior = create_cbs_tree_prior(),
beauti_options = create_beauti_options_v2_6()
)
expect_true(file.exists(output_filename))
expect_false(file.exists(tipdates_filename))
remove_beautier_folder()
})This test is in |
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Note to self:
Attaching the created XML... |
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Note to self: On the other hand, it seems that the absent tipdates file did not make it into the XML at all ...? |
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Note to self: the tipdates file is not stored in the BEAST2 input XML file. Instead, its content is added to the sequences, e.g. So indeed beautier should give an error! |
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Hi @WJH58, Thanks again for this bug report! I think I fixed it. To use the new code, install it with: remotes::install_github("ropensci/beautier", ref = "develop")Could you confirm that now you get a proper error message? I've added you as a contributor of the beautier package as I know how tedious it is to make a proper bug report like that 👍 |
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P.S. the code will reach CRAN when testing has finished and after CRAN has had their (well-deserved) holidays 👍 |
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@richelbilderbeek |
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It is because of the function tipdate_taxa_to_xml_trait(): Only when the version of beast is not 2.6, inference_model$tipdates_filename would be read. However beastierinstall::install_beast2() automatically installs v2.6. I would like to try v2.7 later. |
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update: I changed the beast2 version to 2.7. In this way, create_beast2_input_file() finally reads tipdates file, but run_beast2() reports error due to the conflicts between Java17 and beast2.7 ... Hope you might give me suggestions about which beast2 version to use. Or fix that tipdate_taxa_to_xml_trait() function. I'd be happy to use beast v2.6. |
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Hi @WJH58, Thanks for confirming that the first part of your bug report works (i.e. give an error message if the tipdates file is not found). I will take a look at the second part before Sunday 23:59 and inform you about my progress 👍 |
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Hi @WJH58, this Sunday did not work out. I will take a look at the second part before next Sunday (January 19th) 23:59 and inform you about my progress 👍 |
Describe the bug
Whatever tipdates filename I specify or even when the tipdates file does not exist, create_beast2_input_file() keeps running smoothly and generate a xml file that does not contain any tip dates information.
To Reproduce
Expected behavior
Screenshots
My files if you would like to test
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