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-rw-r--r--NOTES.org137
1 files changed, 66 insertions, 71 deletions
diff --git a/NOTES.org b/NOTES.org
index 7775b5f..7ae5289 100644
--- a/NOTES.org
+++ b/NOTES.org
@@ -48,22 +48,17 @@ 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 table-name="amino-acid-to-codon" range="@<<$<..@>$>" :results verbatim
- (let ((raw-data (org-table-get-remote-range table-name range)))
- (seq-reduce (lambda (acc elt)
- (set-text-properties 0 (length elt) nil elt)
- (if (or (not acc) (cdar acc))
- (cons (list elt) acc)
- (cons (cons (caar acc) (split-string elt)) (cdr acc))))
- raw-data
- nil))
+#+begin_src elisp :var raw-data=amino-acid-to-codon range="@<<$<..@>$>" :results verbatim
+ (mapcar (lambda (kvp)
+ (cons (car kvp) (split-string (cadr kvp))))
+ raw-data)
#+end_src
#+RESULTS: aa-table-to-form
-: (("STOP" "TAA" "TGA" "TAG") ("Val" "GTT" "GTC" "GTA" "GTG") ("Tyr" "TAT" "TAC") ("Trp" "TGG") ("Thr" "ACT" "ACC" "ACA" "ACG") ("Ser" "TCT" "TCC" "TCA" "TCG" "AGT" "AGC") ("Pro" "CCT" "CCC" "CCA" "CCG") ("Phe" "TTT" "TTC") ("Met" "ATG") ("Lys" "AAA" "AAG") ("Leu" "CTT" "CTC" "CTA" "CTG" "TTA" "TTG") ("Ile" "ATT" "ATC" "ATA") ("His" "CAT" "CAC") ("Gly" "GGT" "GGC" "GGA" "GGG") ("Glu" "GAA" "GAG") ("Gln" "CAA" "CAG") ("Cys" "TGT" "TGC") ("Asp" "GAT" "GAC") ("Asn" "AAT" "AAC") ("Arg" "CGT" "CGC" "CGA" "CGG" "AGA" "AGG") ("Ala" "GCT" "GCC" "GCA" "GCG"))
+: (("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 table-name="amino-acid-to-codon" range="@<<$<..@>$>"
+#+begin_src elisp :var raw-data=amino-acid-to-codon range="@<<$<..@>$>"
(let ((codon-alist (mapcar (lambda (aa-to-codons) (cons (cdr aa-to-codons) (car aa-to-codons)))
<<aa-table-to-form>>)))
(apply 'append
@@ -75,10 +70,10 @@ Continue to mutate for 10 rounds, though not all 10 of your sequences will survi
#+end_src
#+RESULTS: aa-table-inverted
-: ((TAA . STOP) (TGA . STOP) (TAG . STOP) (GTT . Val) (GTC . Val) (GTA . Val) (GTG . Val) (TAT . Tyr) (TAC . Tyr) (TGG . Trp) (ACT . Thr) (ACC . Thr) (ACA . Thr) (ACG . Thr) (TCT . Ser) (TCC . Ser) (TCA . Ser) (TCG . Ser) (AGT . Ser) (AGC . Ser) (CCT . Pro) (CCC . Pro) (CCA . Pro) (CCG . Pro) (TTT . Phe) (TTC . Phe) (ATG . Met) (AAA . Lys) (AAG . Lys) (CTT . Leu) (CTC . Leu) (CTA . Leu) (CTG . Leu) (TTA . Leu) (TTG . Leu) (ATT . Ile) (ATC . Ile) (ATA . Ile) (CAT . His) (CAC . His) (GGT . Gly) (GGC . Gly) (GGA . Gly) (GGG . Gly) (GAA . Glu) (GAG . Glu) (CAA . Gln) (CAG . Gln) (TGT . Cys) (TGC . Cys) (GAT . Asp) (GAC . Asp) (AAT . Asn) (AAC . Asn) (CGT . Arg) (CGC . Arg) (CGA . Arg) (CGG . Arg) (AGA . Arg) (AGG . Arg) (GCT . Ala) (GCC . Ala) (GCA . Ala) (GCG . Ala))
+: ((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 table-name="amino-acid-to-codon" range="@<<$<..@>$>"
+#+begin_src elisp :var raw-data=amino-acid-to-codon range="@<<$<..@>$>"
(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")))
@@ -87,70 +82,70 @@ Continue to mutate for 10 rounds, though not all 10 of your sequences will survi
#+RESULTS: tbl-to-json
#+begin_example
{
- 'TAA': 'STOP',
- 'TGA': 'STOP',
- 'TAG': 'STOP',
- 'GTT': 'Val',
- 'GTC': 'Val',
- 'GTA': 'Val',
- 'GTG': 'Val',
- 'TAT': 'Tyr',
- 'TAC': 'Tyr',
- 'TGG': 'Trp',
- 'ACT': 'Thr',
- 'ACC': 'Thr',
- 'ACA': 'Thr',
- 'ACG': 'Thr',
- 'TCT': 'Ser',
- 'TCC': 'Ser',
- 'TCA': 'Ser',
- 'TCG': 'Ser',
- 'AGT': 'Ser',
- 'AGC': 'Ser',
- 'CCT': 'Pro',
- 'CCC': 'Pro',
- 'CCA': 'Pro',
- 'CCG': 'Pro',
- 'TTT': 'Phe',
- 'TTC': 'Phe',
- 'ATG': 'Met',
- 'AAA': 'Lys',
- 'AAG': 'Lys',
- 'CTT': 'Leu',
- 'CTC': 'Leu',
- 'CTA': 'Leu',
- 'CTG': 'Leu',
- 'TTA': 'Leu',
- 'TTG': 'Leu',
- 'ATT': 'Ile',
- 'ATC': 'Ile',
- 'ATA': 'Ile',
- 'CAT': 'His',
- 'CAC': 'His',
- 'GGT': 'Gly',
- 'GGC': 'Gly',
- 'GGA': 'Gly',
- 'GGG': 'Gly',
- 'GAA': 'Glu',
- 'GAG': 'Glu',
- 'CAA': 'Gln',
- 'CAG': 'Gln',
- 'TGT': 'Cys',
- 'TGC': 'Cys',
- 'GAT': 'Asp',
- 'GAC': 'Asp',
- 'AAT': 'Asn',
- 'AAC': 'Asn',
+ 'GCT': 'Ala',
+ 'GCC': 'Ala',
+ 'GCA': 'Ala',
+ 'GCG': 'Ala',
'CGT': 'Arg',
'CGC': 'Arg',
'CGA': 'Arg',
'CGG': 'Arg',
'AGA': 'Arg',
'AGG': 'Arg',
- 'GCT': 'Ala',
- 'GCC': 'Ala',
- 'GCA': 'Ala',
- 'GCG': 'Ala',
+ '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