Re: [R] 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 1801 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 1 301 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_aliSequence 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 ATGAAGAAGATGTTTATGGCGGATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGCGCTA AAGGTTTGAGCCAAGTATAATGAGAATGATACATTCACAGTGTGGCCGGGAGTA CTGGACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGT ``` On Mon, Feb 15, 2021 at 7:28 PM Bill Dunlap wrote: > > > 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 > 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 > > > > __ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. -- Best regards, Luigi __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to load fasta file with openPrimeR?
I think the problem is system.file, which is R base, but I'll go for bioconductor. Thanks On Mon, Feb 15, 2021 at 7:18 PM Bert Gunter wrote: > > As this is a Bioconductor package, why not ask on their support page: > > https://support.bioconductor.org/ > > > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Mon, Feb 15, 2021 at 10:11 AM Luigi Marongiu > 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 >> >> __ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. -- Best regards, Luigi __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to load fasta file with openPrimeR?
> 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 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 > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to load fasta file with openPrimeR?
As this is a Bioconductor package, why not ask on their support page: https://support.bioconductor.org/ Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Mon, Feb 15, 2021 at 10:11 AM Luigi Marongiu 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 > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.