RNA to protein in bash?

Question

[enrique]

Hello everybody.

I'm new in this and I need to do a script in bash that translate a sequence from RNA to protein.

I was using this:

#!/bin/bash

echo "sequence of RNA: $rna "
while read rna ; do

cut=$(echo "${rna}" | sed -n -e 's/\(...\)/\\n/gp'| sed -f dna.sed)
echo "$cut" | tr

dna.sed is another file with the codons.

s/UUU /F /g
s/CUU /L /g
s/AUU /I /g
s/GUU /V /g
..

But I don't know why doesn't work.

Thanks in advance

[iraun]

Is this a homework? Because there are a huge ways to get a protein sequence from a dna one. Furthermore this type of tasks can be done much more easy with bioperl or biopython packages. If you're still interested in writing this kind of script in bash for learning or whatever, you should start writing step by step, and understanding each line code, like:

1) Read rna sequence 3 nt by 3nt
2) Look the 3bp codon in a table/hash/file where the codon -- aa conversion is specified.
3) Write output protein sequence.

[enrique]

Yes, this is a homework. I'm learning to program in different languages and one of the exercises is this.

[Emily]

This is how you ask for help on homework! Other people who just post the question and expect us to do the work for them, take note.

Answer 1

[rioualen]

Hi,

Does it have to be in shell scripting?
Because there are already existing solutions, see R package Biostrings or Biopython for example.

[enrique]

Yes, it's an exercise that has sent me the teacher.

Answer 2

[Benn]

Why don't you use EMBOSS in bash? It has transeq or sixpack methods for translation to proteins.

[enrique]

Because it's an exercise that has sent the teacher. I'm learning to program in different languages and one of the exercises is this.

[Benn]

Okay, does your teacher allow you to ask help on this forum?

[enrique]

He told us that we can look for information anywhere as long as we knew what we were doing. haha

[Benn]

LOL! :D