Load templates from openPrimeR
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@936f2610
Last seen 12 months ago
Mexico

Hi, I tried to uploead my template but I'm having this error, do I need to had an especific format for ma Fasta file?

> 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)
   The number of cores for was set to '2' by 'parallel_setup()'
> fasta.file <- system.file("/Downloads/secuence.fasta", package = "openPrimeR")

> fasta.file
Error: unexpected '>' in ">"
> fasta.file <- system.file("/Downloads/secuence.fasta", package = "openPrimeR")
> fasta.file
[1] ""
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.11.0
LAPACK: /usr/lib/liblapack.so.3.11.0

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

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

other attached packages:
[1] openPrimeR_1.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10             plyr_1.8.8              pillar_1.8.1           
 [4] compiler_4.2.2          RColorBrewer_1.1-3      GenomeInfoDb_1.34.7    
 [7] XVector_0.38.0          bitops_1.0-7            iterators_1.0.14       
[10] tools_4.2.2             zlibbioc_1.44.0         lifecycle_1.0.3        
[13] tibble_3.1.8            gtable_0.3.1            pkgconfig_2.0.3        
[16] rlang_1.0.6             foreach_1.5.2           cli_3.6.0              
[19] GenomeInfoDbData_1.2.9  stringr_1.5.0           dplyr_1.1.0            
[22] Biostrings_2.66.0       generics_0.1.3          S4Vectors_0.36.1       
[25] vctrs_0.5.2             IRanges_2.32.0          stats4_4.2.2           
[28] grid_4.2.2              tidyselect_1.2.0        glue_1.6.2             
[31] R6_2.5.1                fansi_1.0.4             reshape2_1.4.4         
[34] ggplot2_3.4.0           magrittr_2.0.3          codetools_0.2-18       
[37] scales_1.2.1            BiocGenerics_0.44.0     GenomicRanges_1.50.2   
[40] colorspace_2.1-0        utf8_1.2.2              stringi_1.7.12         
[43] lpSolveAPI_5.5.2.0-17.9 RCurl_1.98-1.10         munsell_0.5.0          
[46] crayon_1.5.2           
> fasta.file <- "secuence.fasta"
> seq.df <- read_templates(fasta.file)
Error in read_templates_single(fname, hdr.structure = hdr.structure, delim = delim,  : 
  Unsupported template input file type or error reading data for file: 'secuence.fasta'

My FASTA file has this format, do I have to convert it to .fa?

>NC_000017.11:c41277500-41196312 Homo sapiens chromosome 17, GRCh38.p14 Primary Assembly
GAGGTATAATTAACAAATAAAAATTGTGTATATGTAAGGTATAAAAGGTTATGTTTTGAGGTATATATAT ATATACAGTGTGAAATAATAATATATTTATTAGCTCACATAGTCACCATTTCCTTTTTATTGTTGTGGTG TGAACATTTAAGATCCACTTTCTCAGCAAATTTCAGGTATACAATAAAGTATTTTAAACTATGTCCACAT TAGAGTGCACCAGATCTGCAGAACATATTCGTCTTATATAACTGATGTTGGTCATGAGAATGTGCTAGTT
PCRmultiplex openPrimeR • 593 views
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I also tried this but it isn't working

    > library(openPrimeR)}
Error: unexpected '}' in "library(openPrimeR)}"
>  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)
The number of cores for was set to '2' by 'parallel_setup()'.
> read_templates("secuence.fasta"BRCA1.fasta)
Error: unexpected '&' in "read_templates(&"
> read_templates("/home/Downloads/BRCA1.fasta")
Error: unexpected '&' in "read_templates(&"
> read_templates(quot;/home/Downloads/BRCA1.fastaquot;)
Error: unexpected ';' in "read_templates(quot;"
> read_templates(quot/home/Downloads/BRCA1.fastaquot)
Error in read_templates(quot/home/Downloads/BRCA1.fastaquot) : 
  object 'quot' not found
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Your code is actually incorrect. Try it again with the right quotations, e.g. like this:

read_templates("/home/Downloads/BRCA1.fasta")

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I got the same error

 > read_templates("/home/Downloads/BRCA1.fasta")
    Error in read_templates_single(fname, hdr.structure = hdr.structure, delim = delim,  : 
      Unsupported template input file type or error reading data for file: '/home/Downloads/BRCA1.fasta'

I saw that rdrr.io has this code for the validate templates, I dont know if I need this format or no.

validate_templates <-  function(object) {
# specify minimal set of columns that should be present in a template data frame:
errors <- NULL
required.fields <- list("ID" = "character", "Header" = "character", 
              "Identifier" = c("integer", "numeric"), "Sequence_Length" = c("integer", "numeric"),
              "Group" = "character", "Allowed_Start_fw" = c("integer", "numeric"),
              "Allowed_End_fw" = c("integer", "numeric"), "Allowed_Start_rev" = c("integer", "numeric"),
              "Allowed_End_rev" = c("integer", "numeric"), "Allowed_fw" = "character", "Allowed_rev" = "character",
              "Allowed_Start_fw_initial" = c("integer", "numeric"), "Allowed_End_fw_initial" = c("integer", "numeric"), 
              "Allowed_Start_rev_initial" = c("integer", "numeric"),
              "Allowed_End_rev_initial" = c("integer", "numeric"), "Sequence" = "character",
              "Run" = "character")
if (!is(object, "data.frame")) {
    errors <- c(errors, "Input was no data frame.")
    return(FALSE)
}
possible.fields <- NULL # don't check for additional fields here
check.fields <- check_setting(possible.fields, object, required.fields)
if (is.character(check.fields)) {
    errors <- c(errors, check.fields)
}
if (length(errors) != 0) {
    return(errors) 
} else {
    # ensure that 'Run' is unique
    check.run <- length(unique(object$Run)) <= 1
    if (check.run) {
        return(TRUE)
    } else {
        msg <- "The 'Run' column may only contain a single unique value."
        return(msg)
    }
}
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Case close, it was my error for not putting the correct quotations, thanks for helping me.

> read_templates("/home/lab13/Documents/SantiagoEdilberto/BRCA1.fasta") 
                       ID                  Header   Group Identifier
1 >BRCA8|IGKV1-12*01|H... >BRCA8|IGKV1-12*01|H... default          1
2 >BRCA9|IGKV1-12*02|H... >BRCA9|IGKV1-12*02|H... default          2
3 >BRCA13|IGKV1-12*02|... >BRCA13|IGKV1-12*02|... default          3
  Sequence_Length Allowed_Start_fw Allowed_End_fw Allowed_Start_rev
1             600                1             30               571
2             660                1             30               631
3             600                1             30               571
  Allowed_End_rev              Allowed_fw             Allowed_rev
1             600 ggtcttgccctgttgccagg... tcttggtcatttgacagttc...
2             660 tcaactagaagtttctaaag... catgccaccacacccggtta...
3             600 ccctataagccagaatccag... tcaagcaatcctcccacctt...
  Allowed_Start_fw_ali Allowed_End_fw_ali Allowed_Start_fw_initial
1                    1                 30                        1
2                    1                 30                        1
3                    1                 30                        1
  Allowed_End_fw_initial Allowed_Start_fw_initial_ali
1                     30                            1
2                     30                            1
3                     30                            1
  Allowed_End_fw_initial_ali Allowed_Start_rev_ali Allowed_End_rev_ali
1                         30                   571                 600
2                         30                   631                 660
3                         30                   571                 600
  Allowed_Start_rev_initial Allowed_End_rev_initial
1                       571                     600
2                       631                     660
3                       571                     600
  Allowed_Start_rev_initial_ali Allowed_End_rev_initial_ali
1                           571                         600
2                           631                         660
3                           571                         600
                 Sequence           InputSequence   Run
1 ggtcttgccctgttgccagg... ggtcttgccctgttgccagg... BRCA1
2 tcaactagaagtttctaaag... tcaactagaagtttctaaag... BRCA1
3 ccctataagccagaatccag... ccctataagccagaatccag... BRCA1
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