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Entering edit mode
14 months ago

Hi! im trying to get a list of dna sequences of a list of genes that i got from a RNA-seq analysis. I was reading that fastaR could bring me a solution. Then i installed with this

install.packages("remotes")
remotes::install_github("sethiyap/fastaR")


and then performed this

genelist <- scan("genelist.txt",  what="character", sep=NULL)

faSomeRecords(gene_list=genelist, fasta_file="genoma.fna", outfile="sc_myGenelist.fa")


but i get this error

faSomeRecords(gene_list=genelist, fasta_file="genoma.fna", outfile="sc_myGenelist.fa")
Error in faSomeRecords(gene_list = genelist, fasta_file = "genoma.fna",  :
no se pudo encontrar la función "faSomeRecords"


it is in spanish but means something like "the function faSomeRecords was not found"

What is the problem???

Thank you all!!!

RNA-Seq R software error • 471 views
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Entering edit mode

You installed those modules, but did you load them?

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Entering edit mode

thank you for your answer, this is what i performed to laod the libraries

library("fastaR")
library("sethiyap")
Error in library("sethiyap") : there is no package called ‘sethiyap’
library("sethiyap/fastaR")
Error in library("sethiyap/fastaR") :
there is no package called ‘sethiyap/fastaR’


And i got the same error:

faSomeRecords(gene_list=genelist, fasta_file="genoma.fna", outfile="sc_myGenelist.fa")
Error in faSomeRecords(gene_list = genelist, fasta_file = "genoma.fna",  :
no se pudo encontrar la función "faSomeRecords"


Thank you!

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Entering edit mode

if i perform this

getAnywhere(fastaR)


i get this

no object named ‘fastaR’ was found


Thanks!

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Entering edit mode
14 months ago
Ram 34k

Please read the documentation. The method name is fa_some_records(), not faSomeRecords().

EDIT: I apologize, it looks like they updated their code to use fa_ instead of fa a few months ago, and some online manuals (this one, for example) have not yet caught on. It's always better to read the documentation provided by the author for these github-based packages.

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Entering edit mode

Hello! this was the error! as you wrote here, the method name was incorrect. Thank you so much, i solved the problem partialy. I will open other answer to tell what is the error now. THank you!

1
Entering edit mode

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work.

3
Entering edit mode
14 months ago

So to clarify, library("fastaR") gives you that error? Are you sure it installed properly? I had to manually install a number of dependencies to get it to install properly.

A tried and true method would be to use the getSequence function from biomaRt, which is pretty easy to use.

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Entering edit mode

yes , i did it manually. And i had to install a lot of dependencies to get it right Thank you!

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Entering edit mode
14 months ago

library(fastaR)

genelist <- scan("genelist.txt",  what="character", sep=NULL)

fa_some_records(gene_list=genelist, fasta_file="genoma.fna", outfile="sc_myGenelist.fa")


Thank you!

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Entering edit mode

Thank you for using fastaR package. I have updated the package and documentation. Please refer to it for your future use.

~ Pooja