Question: sethiyap/fastaR --> faSomeRecords was not found
0
gravatar for ovariohisterectomia
3 months ago by
ovariohisterectomia20 wrote:

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 • 213 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by ovariohisterectomia20
1

You installed those modules, but did you load them?

ADD REPLYlink written 3 months ago by WouterDeCoster44k

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 REPLYlink modified 3 months ago by Kevin Blighe63k • written 3 months ago by ovariohisterectomia20

if i perform this

getAnywhere(fastaR)

i get this

no object named ‘fastaR’ was found

Thanks!

ADD REPLYlink modified 3 months ago • written 3 months ago by ovariohisterectomia20
4
gravatar for RamRS
3 months ago by
RamRS28k
Houston, TX
RamRS28k wrote:

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 COMMENTlink modified 3 months ago • written 3 months ago by RamRS28k

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 REPLYlink written 3 months ago by ovariohisterectomia20
1

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 REPLYlink written 3 months ago by RamRS28k
3
gravatar for jared.andrews07
3 months ago by
jared.andrews076.4k
Memphis, TN
jared.andrews076.4k wrote:

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 COMMENTlink written 3 months ago by jared.andrews076.4k

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

ADD REPLYlink written 3 months ago by ovariohisterectomia20
1
gravatar for ovariohisterectomia
3 months ago by
ovariohisterectomia20 wrote:

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 COMMENTlink written 3 months ago by ovariohisterectomia20

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

~ Pooja

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by poojasethiya80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1522 users visited in the last hour