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-rw-r--r--NOTES.org160
1 files changed, 90 insertions, 70 deletions
diff --git a/NOTES.org b/NOTES.org
index 7ae5289..6be8975 100644
--- a/NOTES.org
+++ b/NOTES.org
@@ -48,17 +48,37 @@ Continue to mutate for 10 rounds, though not all 10 of your sequences will survi
| STOP | TAA TGA TAG |
#+name: aa-table-to-form
-#+begin_src elisp :var raw-data=amino-acid-to-codon range="@<<$<..@>$>" :results verbatim
+#+begin_src elisp :var raw-data=amino-acid-to-codon
(mapcar (lambda (kvp)
(cons (car kvp) (split-string (cadr kvp))))
raw-data)
#+end_src
#+RESULTS: aa-table-to-form
-: (("Ala" "GCT" "GCC" "GCA" "GCG") ("Arg" "CGT" "CGC" "CGA" "CGG" "AGA" "AGG") ("Asn" "AAT" "AAC") ("Asp" "GAT" "GAC") ("Cys" "TGT" "TGC") ("Gln" "CAA" "CAG") ("Glu" "GAA" "GAG") ("Gly" "GGT" "GGC" "GGA" "GGG") ("His" "CAT" "CAC") ("Ile" "ATT" "ATC" "ATA") ("Leu" "CTT" "CTC" "CTA" "CTG" "TTA" "TTG") ("Lys" "AAA" "AAG") ("Met" "ATG") ("Phe" "TTT" "TTC") ("Pro" "CCT" "CCC" "CCA" "CCG") ("Ser" "TCT" "TCC" "TCA" "TCG" "AGT" "AGC") ("Thr" "ACT" "ACC" "ACA" "ACG") ("Trp" "TGG") ("Tyr" "TAT" "TAC") ("Val" "GTT" "GTC" "GTA" "GTG") ("STOP" "TAA" "TGA" "TAG"))
+| Ala | GCT | GCC | GCA | GCG | | |
+| Arg | CGT | CGC | CGA | CGG | AGA | AGG |
+| Asn | AAT | AAC | | | | |
+| Asp | GAT | GAC | | | | |
+| Cys | TGT | TGC | | | | |
+| Gln | CAA | CAG | | | | |
+| Glu | GAA | GAG | | | | |
+| Gly | GGT | GGC | GGA | GGG | | |
+| His | CAT | CAC | | | | |
+| Ile | ATT | ATC | ATA | | | |
+| Leu | CTT | CTC | CTA | CTG | TTA | TTG |
+| Lys | AAA | AAG | | | | |
+| Met | ATG | | | | | |
+| Phe | TTT | TTC | | | | |
+| Pro | CCT | CCC | CCA | CCG | | |
+| Ser | TCT | TCC | TCA | TCG | AGT | AGC |
+| Thr | ACT | ACC | ACA | ACG | | |
+| Trp | TGG | | | | | |
+| Tyr | TAT | TAC | | | | |
+| Val | GTT | GTC | GTA | GTG | | |
+| STOP | TAA | TGA | TAG | | | |
#+name: aa-table-inverted
-#+begin_src elisp :var raw-data=amino-acid-to-codon range="@<<$<..@>$>"
+#+begin_src elisp :var raw-data=amino-acid-to-codon
(let ((codon-alist (mapcar (lambda (aa-to-codons) (cons (cdr aa-to-codons) (car aa-to-codons)))
<<aa-table-to-form>>)))
(apply 'append
@@ -73,7 +93,7 @@ Continue to mutate for 10 rounds, though not all 10 of your sequences will survi
: ((GCT . Ala) (GCC . Ala) (GCA . Ala) (GCG . Ala) (CGT . Arg) (CGC . Arg) (CGA . Arg) (CGG . Arg) (AGA . Arg) (AGG . Arg) (AAT . Asn) (AAC . Asn) (GAT . Asp) (GAC . Asp) (TGT . Cys) (TGC . Cys) (CAA . Gln) (CAG . Gln) (GAA . Glu) (GAG . Glu) (GGT . Gly) (GGC . Gly) (GGA . Gly) (GGG . Gly) (CAT . His) (CAC . His) (ATT . Ile) (ATC . Ile) (ATA . Ile) (CTT . Leu) (CTC . Leu) (CTA . Leu) (CTG . Leu) (TTA . Leu) (TTG . Leu) (AAA . Lys) (AAG . Lys) (ATG . Met) (TTT . Phe) (TTC . Phe) (CCT . Pro) (CCC . Pro) (CCA . Pro) (CCG . Pro) (TCT . Ser) (TCC . Ser) (TCA . Ser) (TCG . Ser) (AGT . Ser) (AGC . Ser) (ACT . Thr) (ACC . Thr) (ACA . Thr) (ACG . Thr) (TGG . Trp) (TAT . Tyr) (TAC . Tyr) (GTT . Val) (GTC . Val) (GTA . Val) (GTG . Val) (TAA . STOP) (TGA . STOP) (TAG . STOP))
#+name: tbl-to-json
-#+begin_src elisp :var raw-data=amino-acid-to-codon range="@<<$<..@>$>"
+#+begin_src elisp :var raw-data=amino-acid-to-codon
(let ((json-map (mapcar (lambda (kvp) (format "'%s': '%s'," (car kvp) (cdr kvp)))
<<aa-table-inverted>>)))
(format "{\n%s\n}" (string-join json-map "\n")))
@@ -81,72 +101,72 @@ Continue to mutate for 10 rounds, though not all 10 of your sequences will survi
#+RESULTS: tbl-to-json
#+begin_example
- {
- 'GCT': 'Ala',
- 'GCC': 'Ala',
- 'GCA': 'Ala',
- 'GCG': 'Ala',
- 'CGT': 'Arg',
- 'CGC': 'Arg',
- 'CGA': 'Arg',
- 'CGG': 'Arg',
- 'AGA': 'Arg',
- 'AGG': 'Arg',
- 'AAT': 'Asn',
- 'AAC': 'Asn',
- 'GAT': 'Asp',
- 'GAC': 'Asp',
- 'TGT': 'Cys',
- 'TGC': 'Cys',
- 'CAA': 'Gln',
- 'CAG': 'Gln',
- 'GAA': 'Glu',
- 'GAG': 'Glu',
- 'GGT': 'Gly',
- 'GGC': 'Gly',
- 'GGA': 'Gly',
- 'GGG': 'Gly',
- 'CAT': 'His',
- 'CAC': 'His',
- 'ATT': 'Ile',
- 'ATC': 'Ile',
- 'ATA': 'Ile',
- 'CTT': 'Leu',
- 'CTC': 'Leu',
- 'CTA': 'Leu',
- 'CTG': 'Leu',
- 'TTA': 'Leu',
- 'TTG': 'Leu',
- 'AAA': 'Lys',
- 'AAG': 'Lys',
- 'ATG': 'Met',
- 'TTT': 'Phe',
- 'TTC': 'Phe',
- 'CCT': 'Pro',
- 'CCC': 'Pro',
- 'CCA': 'Pro',
- 'CCG': 'Pro',
- 'TCT': 'Ser',
- 'TCC': 'Ser',
- 'TCA': 'Ser',
- 'TCG': 'Ser',
- 'AGT': 'Ser',
- 'AGC': 'Ser',
- 'ACT': 'Thr',
- 'ACC': 'Thr',
- 'ACA': 'Thr',
- 'ACG': 'Thr',
- 'TGG': 'Trp',
- 'TAT': 'Tyr',
- 'TAC': 'Tyr',
- 'GTT': 'Val',
- 'GTC': 'Val',
- 'GTA': 'Val',
- 'GTG': 'Val',
- 'TAA': 'STOP',
- 'TGA': 'STOP',
- 'TAG': 'STOP',
- }
+{
+'GCT': 'Ala',
+'GCC': 'Ala',
+'GCA': 'Ala',
+'GCG': 'Ala',
+'CGT': 'Arg',
+'CGC': 'Arg',
+'CGA': 'Arg',
+'CGG': 'Arg',
+'AGA': 'Arg',
+'AGG': 'Arg',
+'AAT': 'Asn',
+'AAC': 'Asn',
+'GAT': 'Asp',
+'GAC': 'Asp',
+'TGT': 'Cys',
+'TGC': 'Cys',
+'CAA': 'Gln',
+'CAG': 'Gln',
+'GAA': 'Glu',
+'GAG': 'Glu',
+'GGT': 'Gly',
+'GGC': 'Gly',
+'GGA': 'Gly',
+'GGG': 'Gly',
+'CAT': 'His',
+'CAC': 'His',
+'ATT': 'Ile',
+'ATC': 'Ile',
+'ATA': 'Ile',
+'CTT': 'Leu',
+'CTC': 'Leu',
+'CTA': 'Leu',
+'CTG': 'Leu',
+'TTA': 'Leu',
+'TTG': 'Leu',
+'AAA': 'Lys',
+'AAG': 'Lys',
+'ATG': 'Met',
+'TTT': 'Phe',
+'TTC': 'Phe',
+'CCT': 'Pro',
+'CCC': 'Pro',
+'CCA': 'Pro',
+'CCG': 'Pro',
+'TCT': 'Ser',
+'TCC': 'Ser',
+'TCA': 'Ser',
+'TCG': 'Ser',
+'AGT': 'Ser',
+'AGC': 'Ser',
+'ACT': 'Thr',
+'ACC': 'Thr',
+'ACA': 'Thr',
+'ACG': 'Thr',
+'TGG': 'Trp',
+'TAT': 'Tyr',
+'TAC': 'Tyr',
+'GTT': 'Val',
+'GTC': 'Val',
+'GTA': 'Val',
+'GTG': 'Val',
+'TAA': 'STOP',
+'TGA': 'STOP',
+'TAG': 'STOP',
+}
#+end_example
* work steps