How to save primers in local file in openPrimeR
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Entering edit mode
@marongiuluigi-7134
Last seen 5 weeks ago
European Union

Hello, I have designed some primers with openPrimeR. On the manual, the object with the primers is saved as a temporary file with tempfile(). Is it possible to save it on a local directory of my choice? Thank you


out.file <- tempfile("my_primers", fileext = ".fasta")
write_primers(optimal.primers$opti, out.file)
# Define the FASTA primer file to load <<< this load an external file, I would like to re-open the one I made... <<<<
#                                         ----------------------------------------------------------------------
primer.location <- system.file("extdata", "IMGT_data", "primers", "IGHV", 
                               "Ippolito2012.fasta", package = "openPrimeR")
# Load the primers
primer.df <- read_primers(primer.location, fw.id = "_fw")

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] progress_1.2.2          tidyselect_1.1.0        purrr_0.3.4             reshape2_1.4.4         
 [5] colorspace_2.0-0        DECIPHER_2.18.1         vctrs_0.3.6             generics_0.1.0         
 [9] stats4_4.0.3            blob_1.2.1              XML_3.99-0.5            rlang_0.4.10           
[13] pillar_1.4.7            glue_1.4.2              DBI_1.1.1               BiocGenerics_0.36.0    
[17] bit64_4.0.5             RColorBrewer_1.1-2      GenomeInfoDbData_1.2.4  foreach_1.5.1          
[21] lifecycle_1.0.0         plyr_1.8.6              stringr_1.4.0           zlibbioc_1.36.0        
[25] Biostrings_2.58.0       munsell_0.5.0           gtable_0.3.0            lpSolveAPI_5.5.2.0-17.7
[29] codetools_0.2-18        memoise_2.0.0           IRanges_2.24.1          fastmap_1.1.0          
[33] GenomeInfoDb_1.26.2     parallel_4.0.3          Rcpp_1.0.6              scales_1.1.1           
[37] cachem_1.0.4            S4Vectors_0.28.1        XVector_0.30.0          startupmsg_0.9.6       
[41] bit_4.0.4               ggplot2_3.3.3           hms_1.0.0               stringi_1.5.3          
[45] uniqtag_1.0             dplyr_1.0.4             distr_2.8.0             GenomicRanges_1.42.0   
[49] grid_4.0.3              ade4_1.7-16             tools_4.0.3             bitops_1.0-6           
[53] magrittr_2.0.1          RCurl_1.98-1.2          tibble_3.0.6            RSQLite_2.2.3          
[57] crayon_1.4.1            seqinr_4.2-5            pkgconfig_2.0.3         ellipsis_0.3.1         
[61] MASS_7.3-53.1           prettyunits_1.1.1       rstudioapi_0.13         iterators_1.0.13       
[65] R6_2.5.0                sfsmisc_1.1-8           compiler_4.0.3
openPrimeR • 81 views
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0
Entering edit mode
@marongiuluigi-7134
Last seen 5 weeks ago
European Union

I found it: just use write orimer with the name of the file:

write_primers(primer$opti, "primers.fasta")
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