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Full Discussion: Convert a DNA sequence into Amino Acid
Top Forums Shell Programming and Scripting Convert a DNA sequence into Amino Acid Post 302957294 by cjcox on Thursday 8th of October 2015 06:05:31 PM
Old 10-08-2015
Ok... a bit messy but done very quickly... first I created a sed script (call the file dna.sed):
(you don't need the /g at the end of these... again, created this quicky)

Code:
s/ACC /Thr /g
s/ACA /Thr /g
s/ACG /Thr /g
s/GCT /Ala /g
s/GCC /Ala /g
s/GCA /Ala /g
s/GCG /Ala /g
s/TAT /Tyr /g
s/TAC /Try /g
s/TAA /Stop /g
s/TAG /Stop /g
s/CAT /His /g
s/CAC /His /g
s/CAA /Gln /g
s/CAG /Gln /g
s/AAT /Asn /g
s/AAC /Asn /g
s/AAA /Lys /g
s/AAG /Lys /g
s/GAT /Asp /g
s/GAC /Asp /g
s/GAA /Glu /g
s/GAG /Glu /g
s/TGT /Cys /g
s/TGC /Cys /g
s/TGA /Stop /g
s/TGG /Trp /g
s/CGT /Arg /g
s/CGC /Arg /g
s/CGA /Arg /g
s/CGG /Arg /g
s/AGT /Ser /g
s/AGC /Ser /g
s/AGA /Arg /g
s/AGG /Arg /g
s/GGT /Gly /g
s/GGC /Gly /g
s/GGA /Gly /g
s/GGG /Gly /g

then a script to process DNA sequence lines (assumes sequences each on a line):

Code:
while read dna;do 
  aawork=$(echo "${dna}" |sed -n -e 's/\(...\)/\1 /gp' | sed -f dna.sed)
  echo "$aawork" | sed 's/ //g'
  echo "$aawork" | tr ' ' '\012' | sort | sed '/^$/d' | uniq -c | sed 's/[ ]*\([0-9]*\) \(.*\)/\2: \1/' 
done

again script expects to read the sequences one at a time, you can redirect from a pipe, etc..

In my example below this is just with the sample line you provided.

Code:
$ dna.sh
GCATGCTGCGATAACTTTGGCTGAACTTTGGCTGAAGCATGCTGCGAAACTTTGGCTGAACTTTGGCTG
AlaCysCysAspAsnPheGlyStopThrLeuAlaGluAlaCysCysGluThrLeuAlaGluLeuTrpLeu
Ala: 4
Asn: 1
Asp: 1
Cys: 4
Glu: 3
Gly: 1
Leu: 4
Phe: 1
Stop: 1
Thr: 2
Trp: 1

This User Gave Thanks to cjcox For This Post:
faizlo
 

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LEARN ABOUT DEBIAN

lastal

LASTAL(1)							   User Commands							 LASTAL(1)

NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

       lastal [options] lastdb-name fasta-sequence-file(s)

DESCRIPTION

       Find local sequence alignments.

       Score  options  (default  settings): -r: match score   (DNA: 1, protein: blosum62, 0<Q<5:  6) -q: mismatch cost (DNA: 1, protein: blosum62,
       0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost  (DNA:  1,  pro-
       tein:   2,  0<Q<5:   9)	-c:  unaligned	residue  pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
       (max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments  (x)  -d:  minimum
       score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)

       Cosmetic  options  (default  settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is
       doing -o: output file -f: output format: 0=tabular, 1=maf (1)

       Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity  for
       initial	matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
       step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128	MiB)  -u:  mask  lowercase  during
       extensions: 0=never, 1=gapless,

	      2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)

       -w:  supress  repeats  inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating
       probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output  type:  0=match  counts,  1=gapless,  2=redundant
       gapped, 3=gapped,

	      4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)

       -Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,

	      4=prb, 5=PSSM (0)

REPORTING BUGS

       Report bugs to: last (ATmark) cbrc (dot) jp
       LAST home page: http://last.cbrc.jp/

lastal 199							     May 2012								 LASTAL(1)
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