How to save primers in a local file with openPrimeR
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@936f2610
Last seen 15 months ago
Mexico

I made primers with openPrimeR and following the HTTML I made this:

>  out.file <- tempfile("home/lab13/Documents/SantiagoEdilberto/PRIMERS BRCA1/primers_v1", fileext = ".fasta")
> write_primers(optimal.primers$opti, "primers_v1")
> primer.location <- system.file("home/lab13/Documents/SantiagoEdilberto/PRIMERS BRCA1/primers_v1", package = "openPrimeR")
> primer.df <- read_primers(primer.location, fw.id = "_fw")
Error in read_primers_single(fname, fw.id = fw.id, rev.id = rev.id, merge.ambig = merge.ambig,  : 
  No file found at specified location: 

So I dont know where does the file is or how to save my primers

> sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

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

other attached packages:
[1] openPrimeR_1.16.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2        purrr_0.3.4             reshape2_1.4.4         
 [4] colorspace_2.0-3        DECIPHER_2.22.0         vctrs_0.4.2            
 [7] generics_0.1.3          stats4_4.1.2            blob_1.2.3             
[10] utf8_1.2.2              XML_3.99-0.11           rlang_1.0.6            
[13] pillar_1.8.1            glue_1.6.2              DBI_1.1.3              
[16] BiocGenerics_0.40.0     bit64_4.0.5             RColorBrewer_1.1-3     
[19] GenomeInfoDbData_1.2.7  foreach_1.5.2           lifecycle_1.0.2        
[22] plyr_1.8.7              stringr_1.4.1           zlibbioc_1.40.0        
[25] Biostrings_2.62.0       munsell_0.5.0           gtable_0.3.1           
[28] memoise_2.0.1           lpSolveAPI_5.5.2.0-17.8 codetools_0.2-18       
[31] fastmap_1.1.0           IRanges_2.28.0          doParallel_1.0.17      
[34] GenomeInfoDb_1.30.1     parallel_4.1.2          fansi_1.0.3            
[37] Rcpp_1.0.9              scales_1.2.1            cachem_1.0.6           
[40] S4Vectors_0.32.4        XVector_0.34.0          bit_4.0.4              
[43] ggplot2_3.3.6           stringi_1.7.8           uniqtag_1.0.1          
[46] dplyr_1.0.10            GenomicRanges_1.46.1    grid_4.1.2             
[49] ade4_1.7-19             cli_3.4.1               tools_4.1.2            
[52] bitops_1.0-7            magrittr_2.0.3          RCurl_1.98-1.9         
[55] tibble_3.1.8            RSQLite_2.2.17          crayon_1.5.2           
[58] seqinr_4.2-16           pkgconfig_2.0.3         MASS_7.3-55            
[61] assertthat_0.2.1        iterators_1.0.14        R6_2.5.1               
[64] compiler_4.1.2 
openPrimeR • 391 views
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You have created out.file but when you create the primers_V1 file, you save it in your current directory and not at the out.file location so you should specify it instaed of "primers_V1" alone

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