[Biococoa-dev] BCToolTranslator

[John Timmer]

Incidentally, to aid with debugging I just changed code so that the
description of a codon sequence now produces something like the following:

P(CCN)W(TGG)Y(TAY)A(GCN)R(CGN)R(MGR)Y(TAY)R(MGR)S(TCN)G(GGN)I(ATH)P(CCN)G(GG
N)S(TCN)T(ACN)H(CAY)A(GCN)S(TCN)A(GCN)D(GAY)A(GCN)W(TGG)G(GGN)D(GAY)P(CCN)G(
GGN)R(MGR)F(TTY)E(GAR)C(TGY)F(TTY)V(GTN)W(TGG)*(TAR)S(TCN)K(AAR)S(TCN)G(GGN)
F(TTY)S(TCN)G(GGN)W(TGG)I(ATH)S(TCN)N(AAY)S(TCN)R(MGR)L(YTR)C(TGY)R(CGN)G(GG
N)T(ACN)N(AAY)V(GTN)A(GCN)C(TGY)C(TGY)F(TTY)I(ATH)C(TGY)Q(CAR)*(TGA)C(TGY)S(
TCN)L(CTN)I(ATH)R(MGR)H(CAY)T(ACN)E(GAR)T(ACN)T(ACN)R(MGR)Y(TAY)S(TCN)V(GTN)
Q(CAR)A(GCN)S(AGY)*(TAR)Q(CAR)W(TGG)F(TTY)R(MGR)*(TGA)F(TTY)*(TGA)*(TGA)R(MG
R)R(MGR)S(TCN)*(TGA)W(TGG)R(MGR)D(GAY)C(TGY)N(AAY)N(AAY)S(AGY)E(GAR)*(TGA)*(
TGA)S(TCN)Y(TAY)R(MGR)C(TGY)*(TAR)A(GCN)C(TGY)*(TAR)E(GAR)D(GAY)A(GCN)F(TTY)
K(AAR)P(CCN)R(MGR)I(ATH)R(CGN)*(TAR)A(GCN)L(CTN)*(TAR)K(AAR)K(AAR)K(AAR)A(GC
N)R(MGR)A(GCN)N(AAY)E(GAR)*(TGA)I(ATH)*(TGA)F(TTY)T(ACN)G(GGN)W(TGG)P(CCN)I(
ATH)T(ACN)W(TGG)*(TGA)A(GCN)F(TTY)N(AAY)Y(TAY)A(GCN)*(TAR)A(GCN)S(TCN)*(TAR)
*(TGA)G(GGN)H(CAY)S(TCN)E(GAR)V(GTN)*(TAR)H(CAY)R(CGN)C(TGY)C(TGY)R(MGR)*(TA
R)Q(CAR)N(AAY)L(CTN)K(AAR)S(AGY)*(TGA)Y(TAY)R(MGR)N(AAY)I(ATH)E(GAR)N(AAY)K(
AAR)G(GGN)E(GAR)D(GAY)G(GGN)R(MGR)G(GGN)H(CAY)C(TGY)E(GAR)K(AAR)S(AGY)D(GAY)
R(MGR)D(GAY)E(GAR)P(CCN)*(TAR)A(GCN)F(TTY)G(GGN)K(AAR)T(ACN)I(ATH)Q(CAR)H(CA
Y)T(ACN)I(ATH)R(MGR)*(TAR)D(GAY)T(ACN)D(GAY)G(GGN)F(TTY)F(TTY)T(ACN)A(GCN)K(
AAR)L(CTN)E(GAR)S(TCN)N(AAY)R(MGR)H(CAY)D(GAY)S(TCN)K(AAR)S(TCN)N(AAY)I(ATH)
R(MGR)G(GGN)Q(CAR)Q(CAR)F(TTY)C(TGY)K(AAR)Q(CAR)L(CTN)G(GGN)C(TGY)Y(TAY)F(TT
Y)G(GGN)I(ATH)R(MGR)L(YTR)Q(CAR)C(TGY)F(TTY)*(TGA)S(AGY)?(---)
 
Which is the amino acid followed by the codon triplet.  Does anyone have
suggestions for better readability before I check in the code?

JT
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