sethiyap/fastaR --> faSomeRecords was not found
3
0
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
ADD COMMENT
1
Entering edit mode

You installed those modules, but did you load them?

ADD REPLY
0
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!

ADD REPLY
0
Entering edit mode

if i perform this

getAnywhere(fastaR)

i get this

no object named ‘fastaR’ was found

Thanks!

ADD REPLY
4
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.

ADD COMMENT
0
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!

ADD REPLY
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.

Upvote|Bookmark|Accept

ADD REPLY
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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
14 months ago

Thank you everyone for your answers. Finally it works like this

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!

ADD COMMENT
0
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

ADD REPLY

Login before adding your answer.

Traffic: 2415 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6