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Converting a sequence to FASTA format in R

When i try to convert the seq to fasta format that is without gaps and numbers in R, I get error. It s reading the file but while writing that in fasta format i get an error. Kindly help me with tis

rna-seq
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written by ashamscsoft • ashamscsoft

Please consider the following, they will heighten the probability you'll get a relevant answer fast:

  1. Please use a precise title. "R in bioinformatics" is extremely generic, and is of a kind people would usually avoid.
  2. Please use relevant tags. Your tag has nothing to do with your question
  3. Give us details on what you tried (with the exact commands) and what exact error you saw (with the error message). The devil is in the details.
  4. Proof read your post. This is a scientific forum, please show us that you invest some effort in both trying to solve your problem and in trying to communicate the challenge.
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written by Ram Ram

This the coding i used

############Creating a mutated sequence file
library(seqinr)
require(ade4)
library(Biostrings)
d1<-read.fasta(file = "H1.fasta")
ds1 <- d1[[1]]
write.fasta(new,names=names(x),file="sample.fasta",nbchar=60)

d2<-read.fasta(file = "sample.fasta")
ds2 <- d2[[1]]

And this s the error i get

> write.fasta(new,names=names(x),file="sample.fasta",nbchar=60)
Error in sequence[(nbchar * q + 1):l] : 
  object of type 'closure' is not subsettable

The line which i get error is started with ">"

This is the coding i tried in R nd the error what I got s attached here

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updated by GouthamAtla GouthamAtla • written by ashamscsoft • ashamscsoft

I guess you copy-pasted code from somewhere that doesn't fit, none of the variables you are using in write.fasta is defined in the code before. new is a function, so that is why you are getting the error. Given the input, the message from R is the correct response to incorrect input. Nothing is unexpected here.

Please revise your code and check use of variables to follow the basics of programming.

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written by Michael Dondrup Michael Dondrup

What is new and x in write.fasta ?

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written by GouthamAtla GouthamAtla

Hello ashamscsoft!

We believe that this post does not fit the main topic of this site.

Not a bioinformatics question. Q is lacking basic programming concepts.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Michael Dondrup Michael Dondrup

Instead of closing the question or we should try to help the user formulate it better. As seen above the original poster has followed up on it. Using R to convert a sequence to FASTA format is a bioinformatics question.

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written by Istvan Albert Istvan Albert

I disagree to leave this open, the user has followed up but: as the code he posted shows the solution to what seems to be bioinformatics is simply lack of basic knowledge in programming, or lazy copy pasting or both. I don't think we can help the user further, because we don't know what is to be achieved here, neither do I think that we should teach basic R programming on this site. Feel free to improve the question if you know how.

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written by Michael Dondrup Michael Dondrup

Right but this cuts both way - the same requirement that we ask people to be more considerate and graceful applies to you as well - you are to one asking for help.

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written by Istvan Albert Istvan Albert

Same thing ly i posted in FB too they re getting it rite?

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written by ashamscsoft • ashamscsoft

You're digging a deeper hole. Use better language and better judgement, and maybe you'll do better next time. You'll get nowhere by being rude to people. Michael criticized your programming practice, you attacked his person - there's a huge difference there.

If you really think Facebook matches your frequency better and we are being rude to you, then there's a genuine difference in perspective. I'd like to remind you that no one - Facebook, Biostars or anywhere else - is under obligation to help you. It's just this is a scientific, professional forum and we expect a certain level of professionalism from people here.

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written by Ram Ram

Not ly me many told me tat if people re posting their questions here. Admin is insulting them like u question does not have sense nd ur copied like such stuff. Understand one thing k we re beginners not expert like u people. If we ask doubt try to help instead of insulting k.

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written by ashamscsoft • ashamscsoft

"Your question seems copy-pasted" is not a personal insult. It's a question of professional ethics. There is a growing trend with people calling themselves a "beginner"/"newbie" as an excuse for not following basic etiquette. We are here to help beginners learn, but we're not here to teach beginners professionalism. Please do not attribute to us your lack of initiative and your unwillingness to learn basic etiquette.

What you are accusing us of is personal to me because I for one see a vast majority of questions that are badly phrased or lacking context created by users I can relate to - they are from my country, and I wish they became better over time. Sadly, many don't. Biostars is one of the friendliest professional communities I've seen. If you feel unwelcome here, we wish you all the best wherever you may feel welcome.

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written by Ram Ram

Thank u nd i wil disconnect from here.

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written by ashamscsoft • ashamscsoft

Not ly me many told me tat if people re posting their questions here. Admin is insulting them like u question does not have sense nd ur copied like such stuff. Understand one thing k we re beginners not expert like u people. If we ask doubt try to help instead of insulting k.

• 1 views • link
written by ashamscsoft • ashamscsoft

Hello ashamscsoft!

We believe that this post does not fit the main topic of this site.

Cross posted on FB....

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 1 views • link
written by Michael Dondrup Michael Dondrup

Not ly me many told me tat if people re posting their questions here. Admin is insulting them like u question does not have sense nd ur copied like such stuff. Understand one thing k we re beginners not expert like u people. If we ask doubt try to help instead of insulting k.

• 1 views • link
written by ashamscsoft • ashamscsoft

2 answers

So Istvan wants me to fish in the dark, so I think I now understand what the problem is. First a hint:

Simply copypasting code doesn't take you anywhere, you need at least basic understanding of programming, I am not even saying R-programming. So please don't use code that you don't understand for your analyses.

Here are the rules that you should check and that are violated:

  • If you want to use a variable, you need to assign data to it first (like with dt, vs. x) and in many you also need to declare the variable. Unfortunately, R is not good in enforcing that, but most programming languages do.
  • Don't use reserved words or names of core functions as variable names (new, t, gc, matrix, ...), you will give yourself hell of a time trying to debug or read this code. Unfortunately, again, R has only very few reserved words and even core functions are not protected against overwriting or using for variables.
  • Values assigned to variable A (ds1) do not magically appear to be assigned to another variable B (x) unless you do some really weird stuff.

R is maybe about the worst language to choose to start learning programming (maybe alongside PHP), because it doesn't enforce any of the good programming habits. So maybe, maybe, you want something like:

write.fasta(_ds1_ , names=names(_ds1_), file="sample.fasta", nbchar=60)
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written by Michael Dondrup Michael Dondrup

Michael Dondrup wat ur thinking in your mind. Ur thinking tat u know everything. I have posted the same question in FB i got lot of help. Do u think they re fools nd ur the one who knows everything. And i already said think before u speak. Do u know this is a copy code. Dont judge anyone k. This is for helping people ly not for criticizing understand tat k. If u know u answer otherwise leave it nd mind ur work

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written by ashamscsoft • ashamscsoft

This is unprofessional. This is not how you handle criticism. Your code does look like copy-pasted code. If not, it would have made some sense. It's either that or you gave us random excerpts.

I'm gonna let things cool down before any action might be taken, but I daresay it'll be difficult to get help on online forums if you're this bitter.

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written by Ram Ram

Sorry, I don't get your gibberish... If you got help by posting on FB, the FBI or whatever, good luck with that further, please spare with your attitude, rage, and trolling. It is not principally wise to respond like that, it is extremely impolite, unprofessional, and doesn't take you anywhere. You better get used to that people know more than you in some fields, and that they are able to spot things with ease. That's how it is.

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written by Michael Dondrup Michael Dondrup

I think tis s not for helping the beginners. So bcoz of this admin i wil leave tis biostar. I think tis s not the way admin should respond for the people. Try to help

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written by ashamscsoft • ashamscsoft

I'm not interested in discussing bs. Take my answer or leave, that's up to you.

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written by Michael Dondrup Michael Dondrup

Michael Dondrup wat ur thinking in your mind. Ur thinking tat u know everything. I have posted the same question in FB i got lot of help. Do u think they re fools nd ur the one who knows everything. And i already said think before u speak. Do u know this is a copy code. Dont judge anyone k. This is for helping people ly not for criticizing understand tat k. If u know u answer otherwise leave it nd mind ur work

• 0 views • link
written by ashamscsoft • ashamscsoft

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