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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 302957292 by faizlo on Thursday 8th of October 2015 05:12:58 PM
Old 10-08-2015
Convert a DNA sequence into Amino Acid
I am trying to write a bash script that would be able to read DNA sequences (each line in the file is a sequence) from a file, where sequences are separated by an empty line. I am then to find the amino acid that these DNA sequences encode per codon (each group of three literals.) For example, if I have a file with the sequence:

Code:
   GCATGCTGCGATAACTTTGGCTGAACTTTGGCTGAAGCATGCTGCGAAACTTTGGCTGAACTTTGGCTG

then starting from GCA (first three literals,) I want to decode the DNA into amino acids based on the following table:

Code:
    Codon(s)                  Amino-acid
    TTT,TTC                    Phe
    TTA,TTG,CTT,CTC,CTA,CTG    Leu
    ATT,ATC,ATA                Ile
    ATG                       Met
    GTT,GTC,GTA,GTG            Val
    TCT,TCC,TCA,TCG            Ser
    CCT,CCC,CCA,CCG            Pro
    ACT,ACC,ACA,ACG            Thr
    GCT,GCC,GCA,GCG            Ala
    TAT,TAC                    Tyr
    TAA,TAG                    Stop
    CAT,CAC                    His
    CAA,CAG                    Gln
    AAT,AAC                    Asn
    AAA,AAG                    Lys
    GAT,GAC                   Asp
    GAA,GAG                   Glu
    TGT,TGC                    Cys
    TGA                        Stop
    TGG                        Trp
    CGT,CGC,CGA,CGG            Arg
    AGT,AGC                    Ser
    AGA,AGG                    Arg
    GGT,GGC,GGA,GGG            Gly

that is, I need to get:
Code:
    AlaCysCysAspAsnPheGlyStopThrLeuAlaGluAlaCysCysGluThrLeuAlaGluLeuTrpLeu

Then I need to print the name of each Amino Acid and how many times it was used. For example:

Code:
    Ala: 4
    Cys: 4

and so on. I have 100s of files with DNA sequences in them, but I am not that good at bash. I tried awk and tr but I did not know how to code the table into a bash script.
Last edited by faizlo; 10-08-2015 at 09:08 PM.. Reason: Add CODE tags.
 

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LEARN ABOUT CENTOS

locale::codes::langext

Locale::Codes::LangExt(3)				User Contributed Perl Documentation				 Locale::Codes::LangExt(3)

NAME

       Locale::Codes::LangExt - standard codes for language extension identification

SYNOPSIS

	  use Locale::Codes::LangExt;

	  $lext = code2langext('acm');		       # $lext gets 'Mesopotamian Arabic'
	  $code = langext2code('Mesopotamian Arabic'); # $code gets 'acm'

	  @codes   = all_langext_codes();
	  @names   = all_langext_names();

DESCRIPTION

       The "Locale::Codes::LangExt" module provides access to standard codes used for identifying language extensions, such as those as defined in
       the IANA language registry.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default IANA language
       registry codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language extensions. A code set may be specified using either a name, or
       a constant that is automatically exported by this module.

       For example, the two are equivalent:

	  $lext = code2langext('acm','alpha');
	  $lext = code2langext('acm',LOCALE_LANGEXT_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from the IANA language registry, such as 'acm' for Mesopotamian Arabic.

	   This is the default code set.

ROUTINES

       code2langext ( CODE [,CODESET] )
       langext2code ( NAME [,CODESET] )
       langext_code2code ( CODE ,CODESET ,CODESET2 )
       all_langext_codes ( [CODESET] )
       all_langext_names ( [CODESET] )
       Locale::Codes::LangExt::rename_langext  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangExt::add_langext  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangExt::delete_langext  ( CODE [,CODESET] )
       Locale::Codes::LangExt::add_langext_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangExt::delete_langext_alias  ( NAME )
       Locale::Codes::LangExt::rename_langext_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangExt::add_langext_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangExt::delete_langext_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes::API man page.

SEE ALSO

       Locale::Codes
	   The Locale-Codes distribution.

       Locale::Codes::API
	   The list of functions supported by this module.

       http://www.iana.org/assignments/language-subtag-registry
	   The IANA language subtag registry.

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 2011-2013 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.16.3							    2013-02-27						 Locale::Codes::LangExt(3)
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