RNA to protein in bash?
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
2 answers
Hi,
Does it have to be in shell scripting?
Because there are already existing solutions, see R package Biostrings or Biopython for example.
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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
bioperlorbiopythonpackages. 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.
Yes, this is a homework. I'm learning to program in different languages and one of the exercises is this.
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.