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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

ssake

SSAKE(1)						      General Commands Manual							  SSAKE(1)

NAME

       ssake - assembling millions of very short DNA sequences

SYNOPSIS

       Progressive assembly of millions of short DNA sequences by k-mer search through a prefix tree and 3' extension.

OPTIONS

       -f     Fasta file containing all the [paired (-p 1) / unpaired (-p 0)] reads (required) paired reads must now be separated by ":"

       -s     Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)

       -m     Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16)

       -o     Minimum number of reads needed to call a base during an extension (default -o 3)

       -r     Minimum base ratio used to accept a overhang consensus base (default -r 0.7)

       -t     Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)>

       -p     Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)

       -v     Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)

       -b     Base name for your output files (optional)

       ============ Options below only considered with -p 1 ============

       -d     Mean distance expected/observed between paired-end reads (default -d 200, optional)

       -e     Error (%) allowed on mean distance   e.g. -e 0.75  == distance +/- 75% (default -e 0.75, optional)

       -k     Minimum number of links (read pairs) to compute scaffold (default -k 2, optional)

       -a     Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.70, optional)

       -z     Minimum contig size to track paired-end reads (default -z 50, optional)

       -g     Fasta file containing unpaired sequence reads (optional)

SEE ALSO

       /usr/share/doc/ssake/SSAKE.readme between

AUTHORS

       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   January 2008 							  SSAKE(1)
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