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Replace list of sequence names with sequences from a fasta file using R

I have a list of sequence names (A1, A2, A3, A1, A1, A2 etc) and a fasta file with the names and sequences, and I am trying to find a way to replace each item on the list with the corresponding sequence from the fasta file.

I've used:

test <- sequences[names(sequences) %in% list]

which just extracts A1, A2, A3 and doesn't give me the remaining ones. What am I missing?

list of sequence names:

A1
A2
A3
A1
A1
A2

fasta file:

>A1
ATCATC
>A2
CCCGGG
>A3
GTGTGT
>A4
TCTATC
>A5
ATCTAC

output:

>A1
ATCATC
>A2
CCCGGG
>A3
GTGTGT

Desired output:

ATCATC
CCCGGG
GTGTGT
ATCATC
ATCATC
CCCGGG
r sequence
• 1,855 views • link
updated by Ram Ram • written by shelley.w.peterson • shelley.w.peterson

Please give representative in/output.

• 0 views • link
written by ATpoint ATpoint

list of sequence names:

A1
A2
A3
A1
A1
A2

fasta file:

>A1
ATCATC
>A2
CCCGGG
>A3
GTGTGT
>A4
TCTATC
>A5
ATCTAC

output:

>A1
ATCATC
>A2
CCCGGG
>A3
GTGTGT

Desired output:

ATCATC
CCCGGG
GTGTGT
ATCATC
ATCATC
CCCGGG
• 0 views • link
updated by Ram Ram • written by shelley.w.peterson • shelley.w.peterson
  1. Please format your post better. I've done it for you this time.
  2. This shows what you have and what you need, but not what you've tried. Your single line of R code does not show how you read or write files, so we don't know the packages or functions you're using.
• 0 views • link
written by Ram Ram

Is there an instruction segment for how to properly format a post? I was proud enough of myself for thinking to put in "< br >" when pressing the enter button didn't work. I'm a biologist not a programmer, so I don't know these things.

• 0 views • link
written by shelley.w.peterson • shelley.w.peterson

Apologies, we do not have a manual for the formatting bar yet. You did a great job with the <br> tags, but the formatting bar is your toolbelt for most tasks.

• 0 views • link
written by Ram Ram

Try dedicated fasta/fastq manipulation tools such as: seqtk, seqkit etc. @ shelley.w.peterson. R code as follows:

> library(Biostrings)
> test=readDNAStringSet("test.fa", format = "fasta")
> names=read.csv("file.txt", header = F, stringsAsFactors = F, strip.white = T)
 > names
  V1
1 A1
2 A2
3 A3
4 A1
5 A1
6 A2
> data.frame("sequences"=test[names$V1])
  sequences
1    ATCATC
2    CCCGGG
3    GTGTGT
4    ATCATC
5    ATCATC
6    CCCGGG
• 0 views • link
written by cpad0112 cpad0112

Thanks so much!!!! As someone who is new to coding, sometimes it's hard to figure out if I'm using the wrong tool/command or if I'm using the correct one the wrong way -_-'

• 0 views • link
written by shelley.w.peterson • shelley.w.peterson

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