#!/usr/bin/awk -f
# Fill out a genetic code with nucleotide abiguity codes.

function tryPair( theHash, theCodon, theBase, theFirst, theSecond ) {
  key = gensub( /./, theFirst, theBase, theCodon );
  aa1 = theHash[key];
  key = gensub( /./, theSecond, theBase, theCodon );
  aa2 = theHash[key];
  if ( aa1 && aa1 == aa2 ) {
    return aa1;
  }
  else {
    return 0; # false;
  }
}

function tryTriplet( theHash, theCodon, theBase, theFirst, theSecond, theThird ) {
  key = gensub( /./, theFirst, theBase, theCodon );
  aa1 = theHash[key];
  key = gensub( /./, theSecond, theBase, theCodon );
  aa2 = theHash[key];
  key = gensub( /./, theThird, theBase, theCodon );
  aa3 = theHash[key];
  if ( aa1 && aa1 == aa2 && aa2 == aa3 ) {
    return aa1;
  }
  else {
    return 0; # false;
  }
}

function tryQuadruplet( theHash, theCodon, theBase, theFirst, theSecond, theThird, theFourth ) {
  key = gensub( /./, theFirst, theBase, theCodon );
  aa1 = theHash[key];
  key = gensub( /./, theSecond, theBase, theCodon );
  aa2 = theHash[key];
  key = gensub( /./, theThird, theBase, theCodon );
  aa3 = theHash[key];
  key = gensub( /./, theFourth, theBase, theCodon );
  aa4 = theHash[key];
  if ( aa1 && aa1 == aa2 && aa2 == aa3 && aa3 == aa4 ) {
    return aa1;
  }
  else {
    return 0; # false;
  }
}

function addOne( theHash, theCodon, theBase, theValue, theAminoAcid ) {
  key = gensub( /./, theValue, theBase, theCodon );
  if ( theAminoAcid !~ /^[A-Z*]$/ ) print ">>", theCodon, key, theAminoAcid;
  theHash[key] = theAminoAcid;
}

# theBase must be 1, 2, or 3.
# theCodon is an array of three letters.
# Vary it while holding other positions constant.
function varyOne( theHash, theCodon, theBase ) {
  aa = tryPair( theHash, theCodon, theBase, "a", "c" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "m", aa );
  }
  aa = tryPair( theHash, theCodon, theBase, "a", "g" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "r", aa );
  }
  aa = tryPair( theHash, theCodon, theBase, "a", "u" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "w", aa );
  }
  aa = tryPair( theHash, theCodon, theBase, "c", "g" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "s", aa );
  }
  aa = tryPair( theHash, theCodon, theBase, "c", "u" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "y", aa );
  }
  aa = tryPair( theHash, theCodon, theBase, "g", "u" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "k", aa );
  }
  aa = tryTriplet( theHash, theCodon, theBase, "a", "c", "g" );
# aa = tryPair( theHash, theCodon, theBase, "m", "g" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "v", aa );
  }
  aa = tryTriplet( theHash, theCodon, theBase, "a", "c", "u" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "h", aa );
  }
  aa = tryTriplet( theHash, theCodon, theBase, "a", "g", "u" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "d", aa );
  }
  aa = tryTriplet( theHash, theCodon, theBase, "c", "g", "u" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "b", aa );
  }
  aa = tryQuadruplet( theHash, theCodon, theBase, "a", "c", "g", "u" );
  if ( aa ) {
    addOne( theHash, theCodon, theBase, "n", aa );
  }
}

function varyTwo( theHash, theCodon, theBase ) {
}

function tryCodon( theHash, theCodon ) {
  varyOne( theHash, theCodon, 1 );
  varyOne( theHash, theCodon, 2 );
  varyOne( theHash, theCodon, 3 );
# varyTwo( theHash, theCodon, 1 );
# varyTwo( theHash, theCodon, 2 );
# varyTwo( theHash, theCodon, 3 );
}

function addAmbig( theHash ) {
# tryCodon( theHash, "aaa" );
# tryCodon( theHash, "aac" );
# tryCodon( theHash, "aag" );
# tryCodon( theHash, "aau" );
# tryCodon( theHash, "aca" );
# tryCodon( theHash, "acc" );
# tryCodon( theHash, "acg" );
# tryCodon( theHash, "acu" );
# tryCodon( theHash, "aga" );
# tryCodon( theHash, "agc" );
# tryCodon( theHash, "agg" );
# tryCodon( theHash, "agu" );
# tryCodon( theHash, "aua" );
# tryCodon( theHash, "auc" );
# tryCodon( theHash, "aug" );
# tryCodon( theHash, "auu" );
# tryCodon( theHash, "caa" );
# tryCodon( theHash, "cac" );
# tryCodon( theHash, "cag" );
# tryCodon( theHash, "cau" );
# tryCodon( theHash, "cca" );
# tryCodon( theHash, "ccc" );
# tryCodon( theHash, "ccg" );
# tryCodon( theHash, "ccu" );
# tryCodon( theHash, "cga" );
# tryCodon( theHash, "cgc" );
# tryCodon( theHash, "cgg" );
# tryCodon( theHash, "cgu" );
# tryCodon( theHash, "cua" );
# tryCodon( theHash, "cuc" );
# tryCodon( theHash, "cug" );
# tryCodon( theHash, "cuu" );
# tryCodon( theHash, "gaa" );
# tryCodon( theHash, "gac" );
# tryCodon( theHash, "gag" );
# tryCodon( theHash, "gau" );
# tryCodon( theHash, "gca" );
# tryCodon( theHash, "gcc" );
# tryCodon( theHash, "gcg" );
# tryCodon( theHash, "gcu" );
# tryCodon( theHash, "gga" );
# tryCodon( theHash, "ggc" );
# tryCodon( theHash, "ggg" );
# tryCodon( theHash, "ggu" );
# tryCodon( theHash, "gua" );
# tryCodon( theHash, "guc" );
# tryCodon( theHash, "gug" );
# tryCodon( theHash, "guu" );
# tryCodon( theHash, "uaa" );
# tryCodon( theHash, "uac" );
# tryCodon( theHash, "uag" );
# tryCodon( theHash, "uau" );
# tryCodon( theHash, "uca" );
# tryCodon( theHash, "ucc" );
# tryCodon( theHash, "ucg" );
# tryCodon( theHash, "ucu" );
# tryCodon( theHash, "uga" );
# tryCodon( theHash, "ugc" );
# tryCodon( theHash, "ugg" );
# tryCodon( theHash, "ugu" );
# tryCodon( theHash, "uua" );
# tryCodon( theHash, "uuc" );
# tryCodon( theHash, "uug" );
# tryCodon( theHash, "uuu" );
  for ( c in theHash ) {
    newHash[c] = theHash[c];
  }
  for ( c in newHash ) {
    tryCodon( theHash, c );
  }

# Do it a second time for more codes.
# First we need to clean up the hash.
# Why? How is it getting corrupted?
  for ( x in theHash ) {
    if ( theHash[x] ) {
      ;#OK
    }
    else {
      delete theHash[x];
    }
  }

  for ( c in theHash ) {
    newHash[c] = theHash[c];
  }
  for ( c in newHash ) {
    tryCodon( theHash, c );
  }
# Clean up again.
  for ( x in theHash ) {
    if ( theHash[x] ) {
      ;#OK
    }
    else {
      delete theHash[x];
    }
  }
# Twice seems to be enough.
# I suppose we could keep doing this until the hash refuses to grow.
}

BEGIN {
  frame = 1;
}

END {
  addAmbig( gencode );
  for ( x in gencode ) {
    print x, gencode[x];
  }
}

{
  gencode[$1] = $2;
}