How to load fasta file with openPrimeR?

Thank you. it looks like it worked:
```
fasta.file <- "stx.fa"
seq.df <- read_templates(fasta.file)
fasta.file
[1] "stx.fa"
seq.df
ID                  Header   Group Identifier
Sequence_Length Allowed_Start_fw Allowed_End_fw
1 >MW311073.1 Escheric... >MW311073.1 Escheric... default          1
          180                1             30
  Allowed_Start_rev Allowed_End_rev              Allowed_fw
 Allowed_rev Allowed_Start_fw_ali
1               151             180 atgaagaagatgtttatggc...
cgctggaatctgcaaccgtt...                    1
  Allowed_End_fw_ali Allowed_Start_fw_initial Allowed_End_fw_initial
Allowed_Start_fw_initial_ali
1                 30                        1                     30
                         1
  Allowed_End_fw_initial_ali Allowed_Start_rev_ali Allowed_End_rev_ali
Allowed_Start_rev_initial
1                         30                   151                 180
                      151
  Allowed_End_rev_initial Allowed_Start_rev_initial_ali
Allowed_End_rev_initial_ali                Sequence
1                     180                           151
         180 atgaagaagatgtttatggc...
            InputSequence Run
1 atgaagaagatgtttatggc... stx
```
When the original file stx.fa is:
```
MW311073.1 Escherichia coli strain XP2F shiga toxin 2 (stx2) gene, partial cds
ATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGCGCTA
AAGGTAAAATTGAGTTTTCCAAGTATAATGAGAATGATACATTCACAGTAAAAGTGGCCGGAAAAGAGTA
CTGGACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGT
```

but if I give these commands to a local file:
```
fasta.file <- system.file("extdata", "IMGT_data", "templates",
                "stx.fa", package = "openPrimeR")
fasta.file <- system.file("stx.fa", package = "openPrimeR")
```
where stx.fa il the file I wanted to open and that is present in the
working directly. I get only an empty object.
If "stx.fa" is in fact in the current working directory then use
   fasta.file <- "stx.fa"
system.file() is for accessing files in installed packages.

-Bill

On Mon, Feb 15, 2021 at 10:11 AM Luigi Marongiu
<marongiu.luigi at gmail.com> wrote:
Hello,
I am trying to load a fast file with the package 'openPrimeR'. The
manual (https://www.bioconductor.org/packages/release/bioc/vignettes/openPrimeR/inst/doc/openPrimeR_vignette.html)
says to use:
```
fasta.file <- system.file("extdata", "IMGT_data", "templates",
                "Homo_sapiens_IGH_functional_exon.fasta", package =
"openPrimeR")
# Load the template sequences from 'fasta.file'
seq.df.simple <- read_templates(fasta.file)
```
but if I give these commands to a local file:
```
fasta.file <- system.file("extdata", "IMGT_data", "templates",
                "stx.fa", package = "openPrimeR")
fasta.file <- system.file("stx.fa", package = "openPrimeR")
```
where stx.fa il the file I wanted to open and that is present in the
working directly. I get only an empty object.
What am I getting wrong?
Thank you

--
Best regards,
Luigi

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and provide commented, minimal, self-contained, reproducible code.

Best regards,
Luigi

How to load fasta file with openPrimeR?

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