Entering edit mode
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
You have created
out.file
but when you create theprimers_V1
file, you save it in your current directory and not at theout.file
location so you should specify it instaed of "primers_V1" alone