How to define settings for design primers with openPrimeR?
1
0
Entering edit mode
@marongiuluigi-7134
Last seen 6 weeks ago
European Union

I am trying to design primers with openPrimeR but I don't understand how to set the settings object. I got:

> fasta.file <- "stx.fa"
> seq.df <- read_templates(fasta.file)
> seq.df$Header
[1] ">MW311073.1 Escherichia coli strain XP2F shiga toxin 2 (stx2) gene, partial cds"
> design_primers(
+   seq.df,
+   mode.directionality = "both",
+   settings,
+   init.algo = "naive",
+   opti.algo = "Greedy",
+   required.cvg = 1,
+   timeout = Inf,
+   max.degen = 16,
+   conservation = 1,
+   sample.name = NULL,
+   cur.results.loc = NULL,
+   primer.df = NULL,
+   updateProgress = NULL
+ )
Error in design_primers(seq.df, mode.directionality = "both", settings,  : 
  object 'settings' not found

So I instantiated a settings object:

> settings <- list()
> constraints(settings)$primer_length <- c("min" = 18, "max" = 18)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘constraints’ for signature ‘"list"’
> conOptions(settings)$allowed_mismatches <- 0
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘conOptions’ for signature ‘"list"’

What is the correct way to define the settings for the primers and design them? Thank you

> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] openPrimeR_1.12.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6              plyr_1.8.6              pillar_1.4.7            compiler_4.0.3         
 [5] RColorBrewer_1.1-2      GenomeInfoDb_1.26.2     XVector_0.30.0          prettyunits_1.1.1      
 [9] progress_1.2.2          bitops_1.0-6            iterators_1.0.13        tools_4.0.3            
[13] zlibbioc_1.36.0         lifecycle_1.0.0         tibble_3.0.6            gtable_0.3.0           
[17] pkgconfig_2.0.3         rlang_0.4.10            foreach_1.5.1           rstudioapi_0.13        
[21] parallel_4.0.3          GenomeInfoDbData_1.2.4  stringr_1.4.0           dplyr_1.0.4            
[25] hms_1.0.0               Biostrings_2.58.0       generics_0.1.0          S4Vectors_0.28.1       
[29] vctrs_0.3.6             IRanges_2.24.1          ade4_1.7-16             stats4_4.0.3           
[33] grid_4.0.3              tidyselect_1.1.0        glue_1.4.2              R6_2.5.0               
[37] distr_2.8.0             seqinr_4.2-5            reshape2_1.4.4          ggplot2_3.3.3          
[41] purrr_0.3.4             magrittr_2.0.1          sfsmisc_1.1-8           MASS_7.3-53.1          
[45] scales_1.1.1            codetools_0.2-18        ellipsis_0.3.1          BiocGenerics_0.36.0    
[49] GenomicRanges_1.42.0    colorspace_2.0-0        startupmsg_0.9.6        stringi_1.5.3          
[53] lpSolveAPI_5.5.2.0-17.7 RCurl_1.98-1.2          munsell_0.5.0           crayon_1.4.1
openPrimeR • 129 views
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1
Entering edit mode
@kevin
Last seen 24 minutes ago
Ireland, Republic of

I do not believe settings is a list object. Can you take a look at the vignette under section Loading and writing settings: Loading and writing settings

It is always a good idea to run through a vignette in its entirety before proceeding with your own analysis.

Kevin

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0
Entering edit mode

I see. I tried to upload settings but:

> library("openPrimeR")
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are

                installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
o ViennaRNA (http://www.tbi.univie.ac.at/RNA/)
o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php)
o MAFFT (http://mafft.cbrc.jp/alignment/software/)
o Pandoc (http://pandoc.org)
Warning messages:
1: In fun(libname, pkgname) :
  'Pandoc' is non-functional, since 'pdflatex' is not installed on your system.
2: In parallel_setup(default.nbr.cores) :
  Please install 'doParallel' to use multiple cores.

> list.files(system.file("extdata", "settings", package = "openPrimeR"), pattern = "*\\.xml")
[1] "A_Taq_PCR_design.xml"          "B_Taq_PCR_evaluate.xml"        "C_Taq_PCR_high_stringency.xml"
> settings.xml <- system.file("extdata", "settings", 
+                             "C_Taq_PCR_high_stringency.xml", package = "openPrimeR")
> settings <- read_settings(settings.xml)
Reading settings file: C_Taq_PCR_high_stringency.xml
Due to missing external tools the following constraints were ignored:cross_dimerization,secondary_structure,self_dimerization
Due to missing external tools the following coverage constraints were ignored:coverage_model

what tool am I missing? Which of the packages I did not install are vital for this step? Thank you

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0
Entering edit mode

Actually, it looks like it is working fine. case closed.

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