Description
The goal of this assignment is to recreate the functionality of the tool found at the following webpage: http://web.expasy.org/translate/ This webpage allows you to translate DNA sequence into the encoded amino acids. Note all six possible frames are translated – the three possible forward frames along with the three possible frames of the reverse complement. This tool also allows you to display the sequences in three possible modes: Verbose, Compact, Include nucleotide sequence. Your code should also do this by accepting a single argument that determines which mode that will be used. Your code should then prompt the user for DNA sequence, print out the output, and continue until they want to quit. Your program does not need to accept different genetic codes or perform any color/highlighting to the text in the output. Standard text output is fine. To help you get started, I have created a template script that you must use for your code. Additional functionality or ambiguity is clarified in the comments of that sample code. I have also shown some sample output from the code that I have written for this assignment. Example output: $ python3 Assignment2_Solution.py Invalid number of options Usage: python3 Assignment2_solution.py Mode can be one of the following options: COMPACT VERBOSE DNA $ python3 Assignment2_Solution.py Compact Verbose Invalid number of options Usage: python3 Assignment2_solution.py Mode can be one of the following options: COMPACT VERBOSE DNA $ python3 Assignment2_Solution.py Compac COMPAC not a valid option Usage: python3 Assignment2_solution.py Mode can be one of the following options: COMPACT VERBOSE DNA $ python3 Assignment2_Solution.py Compact Enter DNA sequence (or Exit to quit the program): ;sdja;sdf;lkajsdf Invalid DNA sequence. Characters must be one of A, a, C, c, G, g, T, or t Enter DNA sequence (or Exit to quit the program): ASDJFLS:FJKEWL:LKJFKL: Invalid DNA sequence. Characters must be one of A, a, C, c, G, g, T, or t Enter DNA sequence (or Exit to quit the program): exit $ python3 Assignment2_Solution.py Compact Enter DNA sequence (or Exit to quit the program): ATGACGGAGTACAAGCTTGTGGTAGTTGGAGATGGAGGAGTTGGTAAATCAGCACTCACCATTCAACTCATCCAGAATCACTTTGTCGA AGAATACGACCCGACCATAGAGGACAGCTACAGAAAGCAGGTTGTGATAGACGGTGAGACATGCCTCCTCGACATATTGGATACCGCCG GACAAGAAGAATATTCGGCGATGCGTGATCAGTACATGAGGACAGGCGAAGGATTTCTGTTGGTTTTCGCCGTCAACGAGGCTAAATCT TTCGAGAATGTCGCTAACTACCGCGAGCAGATTCGGAGGGTAAAGGATTCAGATGATGTTCCTATGGTCTTGGTAGGGAATAAATGTGA TTTGTCATCTCGATCAGTCGACTTCCGAACAGTCAGTGAGACAGCAAAGGGTTACGGTATTCCGAATGTCGACACATCTGCCAAAACGC GTATGGGAGTTGATGAAGCATTTTACACACTTGTTAGAGAAATTCGCAAGCATCGTGAGCGTCACGACAATAATAAGCCACAAAAGAAG AAGAAGTGTCAAATAATGTGA 5′ to 3′ Frame: 0 MTEYKLVVVGDGGVGKSALTIQLIQNHFVEEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNEAKS FENVANYREQIRRVKDSDDVPMVLVGNKCDLSSRSVDFRTVSETAKGYGIPNVDTSAKTRMGVDEAFYTLVREIRKHRERHDNNKPQKK KKCQIM5′ to 3′ Frame: 1 -RSTSLW-LEMEELVNQHSPFNSSRITLSKNTTRP-RTATESRL–TVRHASSTYWIPPDKKNIRRCVISTGQAKDFCWFSPSTRLNLSRMSLTTASRFGG-RIQMMFLWSWGINVICHLDQSTSEQSVRQQRVTVFRMSTHLPKRVWELMKHFTHLLEKFASIVSVTTIISHKRRRSVK-C 5′ to 3′ Frame: 2 DGVQACGSWRWRSW-ISTHHSTHPESLCRRIRPDHRGQLQKAGCDRR-DMPPRHIGYRRTRRIFGDA-SVHEDRRRISVGFRRQRGIFRECR-LPRADSEGKGFR-CSYGLGRE-M-FVISISRLPNSQ-DSKGLRYSECRHICQNAYGS–SILHTC-RNSQAS-ASRQ– ATKEEEVSNNV 3′ to 5′ Frame: 0 SHYLTLLLLLWLIIVVTLTMLANFSNKCVKCFINSHTRFGRCVDIRNTVTLCCLTDCSEVD-SR-QITFIPYQDHRNIIILYPPNLLAVVSDILERFSLVDGENQQKSFACPHVLITHRRIFFLSGGIQYVEEACLTVYHNLLSVAVLYGRVVFFDKVILDELNGECFTNSSISNYHKLVLRH 3′ to 5′ Frame: 1 HII-HFFFFCGLLLS-RSRCLRISLTSV-NASSTPIRVLADVSTFGIPPFAVSLTVRKSTDRDDKSHLFPTKTIGTSSESFTLRICSR-LATFSKDLASLTAKTNRNPSPVLMYSRIAEYSSCPAVSNMSRRHVSPSITTCFL-LSSMVGSYSSTK-FWMS-MVSADLPTPPSPTTTSLYSV 3′ to 5′ Frame: 2 TLFDTSSSFVAYYCRDAHDACEFL-QVCKMLHQLPYAFWQMCRHSEYRNPLLSH-LFGSRLIEMTNHIYSLPRPEHHLNPLPSESARGS-RHSRKI-PR-RRKPTEILRLSSCTDHASPNILLVRRYPICRGGMSHRLSQPAFCSCPLWSGRILRQSDSGVEW-VLIYQLLHLQLPQACTPS Enter DNA sequence (or Exit to quit the program): exit $ python3 Assignment2_Solution.py Verbose Enter DNA sequence (or Exit to quit the program): ATGACGGAGTACAAGCTTGTGGTAGTTGGAGATGGAGGAGTTGGTAAATCAGCACTCACCATTCAACTCATCCAGAATCACTTTGTCGA AGAATACGACCCGACCATAGAGGACAGCTACAGAAAGCAGGTTGTGATAGACGGTGAGACATGCCTCCTCGACATATTGGATACCGCCG GACAAGAAGAATATTCGGCGATGCGTGATCAGTACATGAGGACAGGCGAAGGATTTCTGTTGGTTTTCGCCGTCAACGAGGCTAAATCT TTCGAGAATGTCGCTAACTACCGCGAGCAGATTCGGAGGGTAAAGGATTCAGATGATGTTCCTATGGTCTTGGTAGGGAATAAATGTGA TTTGTCATCTCGATCAGTCGACTTCCGAACAGTCAGTGAGACAGCAAAGGGTTACGGTATTCCGAATGTCGACACATCTGCCAAAACGC GTATGGGAGTTGATGAAGCATTTTACACACTTGTTAGAGAAATTCGCAAGCATCGTGAGCGTCACGACAATAATAAGCCACAAAAGAAG AAGAAGTGTCAAATAATGTGA 5′ to 3′ Frame: 0 Met T E Y K L V V V G D G G V G K S A L T I Q L I Q N H F V E E Y D P T I E D S Y R K Q V V I D G E T C L L D I L D T A G Q E E Y S A Met R D Q Y Met R T G E G F L L V F A V N E A K S F E N V A N Y R E Q I R R V K D S D D V P Met V L V G N K C D L S S R S V D F R T V S E T A K G Y G I P N V D T S A K T R Met G V D E A F Y T L V R E I R K H R E R H D N N K P Q K K K K C Q I Met Stop 5′ to 3′ Frame: 1 Stop R S T S L W Stop L E Met E E L V N Q H S P F N S S R I T L S K N T T R P Stop R T A T E S R L Stop Stop T V R H A S S T Y W I P P D K K N I R R C V I S T Stop G Q A K D F C W F S P S T R L N L S R Met S L T T A S R F G G Stop R I Q Met Met F L W S W Stop G I N V I C H L D Q S T S E Q S V R Q Q R V T V F R Met S T H L P K R V W E L Met K H F T H L L E K F A S I V S V T T I I S H K R R R S V K Stop C 5′ to 3′ Frame: 2 D G V Q A C G S W R W R S W Stop I S T H H S T H P E S L C R R I R P D H R G Q L Q K A G C D R R Stop D Met P P R H I G Y R R T R R I F G D A Stop S V H E D R R R I S V G F R R Q R G Stop I F R E C R Stop L P R A D S E G K G F R Stop C S Y G L G R E Stop Met Stop F V I S I S R L P N S Q Stop D S K G L R Y S E C R H I C Q N A Y G S Stop Stop S I L H T C Stop R N S Q A S Stop A S R Q Stop Stop A T K E E E V S N N V 3′ to 5′ Frame: 0 S H Y L T L L L L L W L I I V V T L T Met L A N F S N K C V K C F I N S H T R F G R C V D I R N T V T L C C L T D C S E V D Stop S R Stop Q I T F I P Y Q D H R N I I Stop I L Y P P N L L A V V S D I L E R F S L V D G E N Q Q K S F A C P H V L I T H R R I F F L S G G I Q Y V E E A C L T V Y H N L L S V A V L Y G R V V F F D K V I L D E L N G E C Stop F T N S S I S N Y H K L V L R H 3′ to 5′ Frame: 1 H I I Stop H F F F F C G L L L S Stop R S R C L R I S L T S V Stop N A S S T P I R V L A D V S T F G I P Stop P F A V S L T V R K S T D R D D K S H L F P T K T I G T S S E S F T L R I C S R Stop L A T F S K D L A S L T A K T N R N P S P V L Met Y Stop S R I A E Y S S C P A V S N Met S R R H V S P S I T T C F L Stop L S S Met V G S Y S S T K Stop F W Met S Stop Met V S A D L P T P P S P T T T S L Y S V 3′ to 5′ Frame: 2 T L F D T S S S F V A Y Y C R D A H D A C E F L Stop Q V C K Met L H Q L P Y A F W Q Met C R H S E Y R N P L L S H Stop L F G S R L I E Met T N H I Y S L P R P Stop E H H L N P L P S E S A R G S Stop R H S R K I Stop P R Stop R R K P T E I L R L S S C T D H A S P N I L L V R R Y P I C R G G Met S H R L S Q P A F C S C P L W S G R I L R Q S D S G Stop V E W Stop V L I Y Q L L H L Q L P Q A C T P S Enter DNA sequence (or Exit to quit the program): exit $ python3 Assignment2_Solution.py DNA Enter DNA sequence (or Exit to quit the program): ATGACGGAGTACAAGCTTGTGGTAGTTGGAGATGGAGGAGTTGGTAAATCAGCACTCACCATTCAACTCATCCAGAATCACTTTGTCGA AGAATACGACCCGACCATAGAGGACAGCTACAGAAAGCAGGTTGTGATAGACGGTGAGACATGCCTCCTCGACATATTGGATACCGCCG GACAAGAAGAATATTCGGCGATGCGTGATCAGTACATGAGGACAGGCGAAGGATTTCTGTTGGTTTTCGCCGTCAACGAGGCTAAATCT TTCGAGAATGTCGCTAACTACCGCGAGCAGATTCGGAGGGTAAAGGATTCAGATGATGTTCCTATGGTCTTGGTAGGGAATAAATGTGA TTTGTCATCTCGATCAGTCGACTTCCGAACAGTCAGTGAGACAGCAAAGGGTTACGGTATTCCGAATGTCGACACATCTGCCAAAACGC GTATGGGAGTTGATGAAGCATTTTACACACTTGTTAGAGAAATTCGCAAGCATCGTGAGCGTCACGACAATAATAAGCCACAAAAGAAG AAGAAGTGTCAAATAATGTGA 5′ to 3′ Frame: 0 ATGACGGAGTACAAGCTTGTGGTAGTTGGAGATGGAGGAGTTGGTAAATCAGCACTCACC M T E Y K L V V V G D G G V G K S A L T ATTCAACTCATCCAGAATCACTTTGTCGAAGAATACGACCCGACCATAGAGGACAGCTAC I Q L I Q N H F V E E Y D P T I E D S Y AGAAAGCAGGTTGTGATAGACGGTGAGACATGCCTCCTCGACATATTGGATACCGCCGGA R K Q V V I D G E T C L L D I L D T A G CAAGAAGAATATTCGGCGATGCGTGATCAGTACATGAGGACAGGCGAAGGATTTCTGTTG Q E E Y S A M R D Q Y M R T G E G F L L GTTTTCGCCGTCAACGAGGCTAAATCTTTCGAGAATGTCGCTAACTACCGCGAGCAGATT V F A V N E A K S F E N V A N Y R E Q I CGGAGGGTAAAGGATTCAGATGATGTTCCTATGGTCTTGGTAGGGAATAAATGTGATTTG R R V K D S D D V P M V L V G N K C D L TCATCTCGATCAGTCGACTTCCGAACAGTCAGTGAGACAGCAAAGGGTTACGGTATTCCG S S R S V D F R T V S E T A K G Y G I P AATGTCGACACATCTGCCAAAACGCGTATGGGAGTTGATGAAGCATTTTACACACTTGTT N V D T S A K T R M G V D E A F Y T L V AGAGAAATTCGCAAGCATCGTGAGCGTCACGACAATAATAAGCCACAAAAGAAGAAGAAG R E I R K H R E R H D N N K P Q K K K K TGTCAAATAATGTGA C Q I M – 5′ to 3′ Frame: 1 TGACGGAGTACAAGCTTGTGGTAGTTGGAGATGGAGGAGTTGGTAAATCAGCACTCACCA – R S T S L W – L E M E E L V N Q H S P TTCAACTCATCCAGAATCACTTTGTCGAAGAATACGACCCGACCATAGAGGACAGCTACA F N S S R I T L S K N T T R P – R T A T GAAAGCAGGTTGTGATAGACGGTGAGACATGCCTCCTCGACATATTGGATACCGCCGGAC E S R L – – T V R H A S S T Y W I P P D AAGAAGAATATTCGGCGATGCGTGATCAGTACATGAGGACAGGCGAAGGATTTCTGTTGG K K N I R R C V I S T – G Q A K D F C W TTTTCGCCGTCAACGAGGCTAAATCTTTCGAGAATGTCGCTAACTACCGCGAGCAGATTC F S P S T R L N L S R M S L T T A S R F GGAGGGTAAAGGATTCAGATGATGTTCCTATGGTCTTGGTAGGGAATAAATGTGATTTGT G G – R I Q M M F L W S W – G I N V I C CATCTCGATCAGTCGACTTCCGAACAGTCAGTGAGACAGCAAAGGGTTACGGTATTCCGA H L D Q S T S E Q S V R Q Q R V T V F R ATGTCGACACATCTGCCAAAACGCGTATGGGAGTTGATGAAGCATTTTACACACTTGTTA M S T H L P K R V W E L M K H F T H L L GAGAAATTCGCAAGCATCGTGAGCGTCACGACAATAATAAGCCACAAAAGAAGAAGAAGT E K F A S I V S V T T I I S H K R R R S GTCAAATAATGT V K – C 5′ to 3′ Frame: 2 GACGGAGTACAAGCTTGTGGTAGTTGGAGATGGAGGAGTTGGTAAATCAGCACTCACCAT D G V Q A C G S W R W R S W – I S T H H TCAACTCATCCAGAATCACTTTGTCGAAGAATACGACCCGACCATAGAGGACAGCTACAG S T H P E S L C R R I R P D H R G Q L Q AAAGCAGGTTGTGATAGACGGTGAGACATGCCTCCTCGACATATTGGATACCGCCGGACA K A G C D R R – D M P P R H I G Y R R T AGAAGAATATTCGGCGATGCGTGATCAGTACATGAGGACAGGCGAAGGATTTCTGTTGGT R R I F G D A – S V H E D R R R I S V G TTTCGCCGTCAACGAGGCTAAATCTTTCGAGAATGTCGCTAACTACCGCGAGCAGATTCG F R R Q R G – I F R E C R – L P R A D S GAGGGTAAAGGATTCAGATGATGTTCCTATGGTCTTGGTAGGGAATAAATGTGATTTGTC E G K G F R – C S Y G L G R E – M – F V ATCTCGATCAGTCGACTTCCGAACAGTCAGTGAGACAGCAAAGGGTTACGGTATTCCGAA I S I S R L P N S Q – D S K G L R Y S E TGTCGACACATCTGCCAAAACGCGTATGGGAGTTGATGAAGCATTTTACACACTTGTTAG C R H I C Q N A Y G S – – S I L H T C – AGAAATTCGCAAGCATCGTGAGCGTCACGACAATAATAAGCCACAAAAGAAGAAGAAGTG R N S Q A S – A S R Q – – A T K E E E V TCAAATAATGTG S N N V 3′ to 5′ Frame: 0 TCACATTATTTGACACTTCTTCTTCTTTTGTGGCTTATTATTGTCGTGACGCTCACGATG S H Y L T L L L L L W L I I V V T L T M CTTGCGAATTTCTCTAACAAGTGTGTAAAATGCTTCATCAACTCCCATACGCGTTTTGGC L A N F S N K C V K C F I N S H T R F G AGATGTGTCGACATTCGGAATACCGTAACCCTTTGCTGTCTCACTGACTGTTCGGAAGTC R C V D I R N T V T L C C L T D C S E V GACTGATCGAGATGACAAATCACATTTATTCCCTACCAAGACCATAGGAACATCATCTGA D – S R – Q I T F I P Y Q D H R N I I – ATCCTTTACCCTCCGAATCTGCTCGCGGTAGTTAGCGACATTCTCGAAAGATTTAGCCTC I L Y P P N L L A V V S D I L E R F S L GTTGACGGCGAAAACCAACAGAAATCCTTCGCCTGTCCTCATGTACTGATCACGCATCGC V D G E N Q Q K S F A C P H V L I T H R CGAATATTCTTCTTGTCCGGCGGTATCCAATATGTCGAGGAGGCATGTCTCACCGTCTAT R I F F L S G G I Q Y V E E A C L T V Y CACAACCTGCTTTCTGTAGCTGTCCTCTATGGTCGGGTCGTATTCTTCGACAAAGTGATT H N L L S V A V L Y G R V V F F D K V I CTGGATGAGTTGAATGGTGAGTGCTGATTTACCAACTCCTCCATCTCCAACTACCACAAG L D E L N G E C – F T N S S I S N Y H K CTTGTACTCCGTCAT L V L R H 3′ to 5′ Frame: 1 CACATTATTTGACACTTCTTCTTCTTTTGTGGCTTATTATTGTCGTGACGCTCACGATGC H I I – H F F F F C G L L L S – R S R C TTGCGAATTTCTCTAACAAGTGTGTAAAATGCTTCATCAACTCCCATACGCGTTTTGGCA L R I S L T S V – N A S S T P I R V L A GATGTGTCGACATTCGGAATACCGTAACCCTTTGCTGTCTCACTGACTGTTCGGAAGTCG D V S T F G I P – P F A V S L T V R K S ACTGATCGAGATGACAAATCACATTTATTCCCTACCAAGACCATAGGAACATCATCTGAA T D R D D K S H L F P T K T I G T S S E TCCTTTACCCTCCGAATCTGCTCGCGGTAGTTAGCGACATTCTCGAAAGATTTAGCCTCG S F T L R I C S R – L A T F S K D L A S TTGACGGCGAAAACCAACAGAAATCCTTCGCCTGTCCTCATGTACTGATCACGCATCGCC L T A K T N R N P S P V L M Y – S R I A GAATATTCTTCTTGTCCGGCGGTATCCAATATGTCGAGGAGGCATGTCTCACCGTCTATC E Y S S C P A V S N M S R R H V S P S I ACAACCTGCTTTCTGTAGCTGTCCTCTATGGTCGGGTCGTATTCTTCGACAAAGTGATTC T T C F L – L S S M V G S Y S S T K – F TGGATGAGTTGAATGGTGAGTGCTGATTTACCAACTCCTCCATCTCCAACTACCACAAGC W M S – M V S A D L P T P P S P T T T S TTGTACTCCGTC L Y S V 3′ to 5′ Frame: 2 ACATTATTTGACACTTCTTCTTCTTTTGTGGCTTATTATTGTCGTGACGCTCACGATGCT T L F D T S S S F V A Y Y C R D A H D A TGCGAATTTCTCTAACAAGTGTGTAAAATGCTTCATCAACTCCCATACGCGTTTTGGCAG C E F L – Q V C K M L H Q L P Y A F W Q ATGTGTCGACATTCGGAATACCGTAACCCTTTGCTGTCTCACTGACTGTTCGGAAGTCGA M C R H S E Y R N P L L S H – L F G S R CTGATCGAGATGACAAATCACATTTATTCCCTACCAAGACCATAGGAACATCATCTGAAT L I E M T N H I Y S L P R P – E H H L N CCTTTACCCTCCGAATCTGCTCGCGGTAGTTAGCGACATTCTCGAAAGATTTAGCCTCGT P L P S E S A R G S – R H S R K I – P R TGACGGCGAAAACCAACAGAAATCCTTCGCCTGTCCTCATGTACTGATCACGCATCGCCG – R R K P T E I L R L S S C T D H A S P AATATTCTTCTTGTCCGGCGGTATCCAATATGTCGAGGAGGCATGTCTCACCGTCTATCA N I L L V R R Y P I C R G G M S H R L S CAACCTGCTTTCTGTAGCTGTCCTCTATGGTCGGGTCGTATTCTTCGACAAAGTGATTCT Q P A F C S C P L W S G R I L R Q S D S GGATGAGTTGAATGGTGAGTGCTGATTTACCAACTCCTCCATCTCCAACTACCACAAGCT G – V E W – V L I Y Q L L H L Q L P Q A TGTACTCCGTCA C T P S Enter DNA sequence (or Exit to quit the program): exit
