How to extract FASTA headers in R
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6 months ago
WUSCHEL ▴ 720

I have downloaded a reference uniprotkb FASTA file. How can I only extract the FASTA headers of each gene (raw-wise) into a CSV file using R?

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I came across this handy tool. CSVā¬ŒFASTA https://cdcgov.github.io/CSV2FASTA/

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This does not answer your question - it does not use R. Please accept the answer that addresses your question, do not add answers that explicitly break a requirement without specifying that the requirement is broken.

I'm moving this answer to a comment now.

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6 months ago
cfos4698 ▴ 830

Here's one example using R:

library(seqinr)
fa <- read.fasta(file = "samples.fasta",   seqtype = "DNA")
CON=file("output.csv", "w")
writeLines("genes", CON)
writeLines(names(fa), CON)
close(CON)

However, is R necessary in this case? Can you just use simpler UNIX tools?

echo "genes" > output.csv
grep ">" samples.fasta | cut -c2- >> output.csv

edit: if you want specific parts of the fasta headers, you will need to be more specific in your question

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