Chubek · October 20, 2023 13:12 · Oct 20, 2023 · Oct 20, 2023
diff --git a/README.md b/README.md
@@ -1,4 +1,12 @@
-The file `triplet.awk` is a nucleotide triplet counter written in AWK. For the uninitiated, AWK is a language designed by Keringhan and Aho at Bell Labs. Today there are many AWK interpreters, and I am making my own interpreter, you can view the project [here](https://github.com/Chubek/Squawk).
+The file `triplet.awk` is a nucleotide triplet counter written in AWK. It's very simple, and has been generated by Python. For the uninitiated, AWK is a language designed by Keringhan and Aho at Bell Labs. Today there are many AWK interpreters, and I am making my own AWK interpreter, you can view the project [here](https://github.com/Chubek/Squawk).
+
+First:
+
+```
+wget https://gist.githubusercontent.com/Chubek/db779e5d92aadccbca1a8a25b4a55e20/raw/f3256185f4a43920b031af29dc9e45cdc1da9871/triplet.awk
+```
+
+... to download the script file.
 
 `triplet.awk` does not care if your file is FASTA, FASTAQ, or whatever else. It just sees triplets, counts them, and displays them at the end. Imagine we have this FASTA file:
 
@@ -106,6 +114,6 @@ You could also:
 awk -f triplet.awk seq.fa [..more files can be added here]
 ```
 
-This script has been written as a gift for my friend Kevin whom I owe a lot to. But I will post it on r/bioinformatics as well. The script is under Unlicense license, you can do whatever you want with it!
+This script has been written as a gift for my friend Kevin whom I owe a lot to. But I will post it on r/bioinformatics as well. The script is under Unlicense license, you can do whatever you want with it! In the future I will make more biotech stuff. I already have 4 projects brewing, you can view them in the list of my repositories.
 
 Thanks, Chubak.
diff --git a/README.md b/README.md
@@ -0,0 +1,111 @@
+The file `triplet.awk` is a nucleotide triplet counter written in AWK. For the uninitiated, AWK is a language designed by Keringhan and Aho at Bell Labs. Today there are many AWK interpreters, and I am making my own interpreter, you can view the project [here](https://github.com/Chubek/Squawk).
+
+`triplet.awk` does not care if your file is FASTA, FASTAQ, or whatever else. It just sees triplets, counts them, and displays them at the end. Imagine we have this FASTA file:
+
+```
+>ref|NC_005213.1|:c879-490883
+ATGCGATTGCTATTAGAACTTAAAGCCCTAAATAGCATAGATAAAAAACAATTATCTAACTATCTAATAC
+AAGGTTTCATTTATAATATATTAAAAAATACCGAATACTCTTGGTTACATAATTGGAAGAAAGAGAAATA
+TTTTAATTTTACCTTAATCCCAAAAAAAGACATAATAGAGAATAAGAGGTATTATTTAATCATATCTTCG
+CCCGATAAAAGGTTTATAGAGGTTTTGCATAATAAAATAAAAGATTTAGATATAATAACTATTGGTTTGG
+CTCAATTCCAATTAAGGAAAACAAAAAAATTCGATCCAAAATTAAGATTTCCTTGGGTTACTATAACTCC
+TATAGTATTAAGGGAAGGCAAAATAGTAATATTAAAAGGGGACAAATACTATAAGGTATTTGTTAAGCGA
+TTGGAAGAATTGAAAAAGTATAATCTAATAAAAAAGAAAGAGCCCATTTTAGAAGAACCCATAGAGATTA
+GTTTAAACCAAATCAAAGATGGATGGAAAATTATAGATGTAAAAGATAGGTATTACGATTTTAGAAATAA
+GAGTTTTAGCGCTTTTTCTAATTGGTTGCGAGACCTAAAAGAGCAAAGCTTAAGAAAATATAATAATTTC
+TGTGGGAAGAACTTTTATTTTGAAGAAGCAATATTCGAAGGTTTTACTTTCTATAAAACAGTATCAATAA
+GAATAAGAATTAACAGAGGGGAAGCAGTATATATAGGCACATTATGGAAAGAGTTAAATGTTTATAGAAA
+ATTAGACAAAGAAGAAAGAGAATTTTACAAATTTTTGTACGATTGCGGTTTGGGTTCATTAAATTCTATG
+GGTTTTGGGTTTGTTAATACAAAAAAGAACTCTGCGAGATAA
+>ref|NC_005213.1|:883-2691
+ATGAAAAAGCCCCAACCCTATAAAGATGAAGAGATATATTCTATTTTAGAAGAGCCCGTAAAACAATGGT
+TTAAAGAGAAATACAAAACATTCACTCCCCCACAAAGGTATGCAATAATGGAAATACATAAAAGGAACAA
+TGTTTTAATTTCTTCCCCCACAGGTTCGGGAAAAACGTTAGCAGCGTTTTTAGCTATAATAAATGAATTA
+ATAAAGTTATCTCATAAAGGAAAATTAGAAAATAGAGTTTATGCCATTTATGTTTCTCCATTAAGAAGTT
+TAAATAACGATGTAAAGAAAAACTTAGAAACTCCATTAAAAGAAATAAAAGAAAAAGCGAAAGAGCTTAA 
+```
+
+We can save this in a file called `seq.fa` and then:
+
+```
+cat seq.fa | awk -f triplet.awk
+```
+
+We will see:
+
+```
+AAA = 18
+AAC = 12
+AAT = 18
+AAG = 17
+ACA = 12
+ACC = 6
+ACT = 9
+ACG = 4
+ATA = 17
+ATC = 7
+ATT = 17
+ATG = 9
+AGA = 16
+AGC = 9
+AGT = 6
+AGG = 11
+CAA = 11
+CAC = 3
+CAT = 10
+CAG = 3
+CCA = 9
+CCC = 7
+CCT = 5
+CCG = 3
+CTA = 10
+CTC = 6
+CTT = 8
+CTG = 1
+CGA = 11
+CGC = 1
+CGT = 2
+CGG = 2
+TAA = 18
+TAC = 10
+TAT = 16
+TAG = 13
+TCA = 8
+TCC = 6
+TCT = 11
+TCG = 4
+TTA = 18
+TTC = 10
+TTT = 15
+TTG = 10
+TGA = 4
+TGC = 7
+TGT = 9
+TGG = 12
+GAA = 17
+GAC = 4
+GAT = 9
+GAG = 12
+GCA = 8
+GCC = 4
+GCT = 4
+GCG = 7
+GTA = 10
+GTC = 0
+GTT = 12
+GTG = 1
+GGA = 10
+GGC = 2
+GGT = 13
+GGG = 7
+```
+
+You could also:
+
+```
+awk -f triplet.awk seq.fa [..more files can be added here]
+```
+
+This script has been written as a gift for my friend Kevin whom I owe a lot to. But I will post it on r/bioinformatics as well. The script is under Unlicense license, you can do whatever you want with it!
+
+Thanks, Chubak.
diff --git a/triplet.awk b/triplet.awk
@@ -0,0 +1,128 @@
+/AAA/{ aaa++; }
+/AAC/{ aac++; }
+/AAT/{ aat++; }
+/AAG/{ aag++; }
+/ACA/{ aca++; }
+/ACC/{ acc++; }
+/ACT/{ act++; }
+/ACG/{ acg++; }
+/ATA/{ ata++; }
+/ATC/{ atc++; }
+/ATT/{ att++; }
+/ATG/{ atg++; }
+/AGA/{ aga++; }
+/AGC/{ agc++; }
+/AGT/{ agt++; }
+/AGG/{ agg++; }
+/CAA/{ caa++; }
+/CAC/{ cac++; }
+/CAT/{ cat++; }
+/CAG/{ cag++; }
+/CCA/{ cca++; }
+/CCC/{ ccc++; }
+/CCT/{ cct++; }
+/CCG/{ ccg++; }
+/CTA/{ cta++; }
+/CTC/{ ctc++; }
+/CTT/{ ctt++; }
+/CTG/{ ctg++; }
+/CGA/{ cga++; }
+/CGC/{ cgc++; }
+/CGT/{ cgt++; }
+/CGG/{ cgg++; }
+/TAA/{ taa++; }
+/TAC/{ tac++; }
+/TAT/{ tat++; }
+/TAG/{ tag++; }
+/TCA/{ tca++; }
+/TCC/{ tcc++; }
+/TCT/{ tct++; }
+/TCG/{ tcg++; }
+/TTA/{ tta++; }
+/TTC/{ ttc++; }
+/TTT/{ ttt++; }
+/TTG/{ ttg++; }
+/TGA/{ tga++; }
+/TGC/{ tgc++; }
+/TGT/{ tgt++; }
+/TGG/{ tgg++; }
+/GAA/{ gaa++; }
+/GAC/{ gac++; }
+/GAT/{ gat++; }
+/GAG/{ gag++; }
+/GCA/{ gca++; }
+/GCC/{ gcc++; }
+/GCT/{ gct++; }
+/GCG/{ gcg++; }
+/GTA/{ gta++; }
+/GTC/{ gtc++; }
+/GTT/{ gtt++; }
+/GTG/{ gtg++; }
+/GGA/{ gga++; }
+/GGC/{ ggc++; }
+/GGT/{ ggt++; }
+/GGG/{ ggg++; }
+END { printf "AAA = %d\n",aaa; }
+END { printf "AAC = %d\n",aac; }
+END { printf "AAT = %d\n",aat; }
+END { printf "AAG = %d\n",aag; }
+END { printf "ACA = %d\n",aca; }
+END { printf "ACC = %d\n",acc; }
+END { printf "ACT = %d\n",act; }
+END { printf "ACG = %d\n",acg; }
+END { printf "ATA = %d\n",ata; }
+END { printf "ATC = %d\n",atc; }
+END { printf "ATT = %d\n",att; }
+END { printf "ATG = %d\n",atg; }
+END { printf "AGA = %d\n",aga; }
+END { printf "AGC = %d\n",agc; }
+END { printf "AGT = %d\n",agt; }
+END { printf "AGG = %d\n",agg; }
+END { printf "CAA = %d\n",caa; }
+END { printf "CAC = %d\n",cac; }
+END { printf "CAT = %d\n",cat; }
+END { printf "CAG = %d\n",cag; }
+END { printf "CCA = %d\n",cca; }
+END { printf "CCC = %d\n",ccc; }
+END { printf "CCT = %d\n",cct; }
+END { printf "CCG = %d\n",ccg; }
+END { printf "CTA = %d\n",cta; }
+END { printf "CTC = %d\n",ctc; }
+END { printf "CTT = %d\n",ctt; }
+END { printf "CTG = %d\n",ctg; }
+END { printf "CGA = %d\n",cga; }
+END { printf "CGC = %d\n",cgc; }
+END { printf "CGT = %d\n",cgt; }
+END { printf "CGG = %d\n",cgg; }
+END { printf "TAA = %d\n",taa; }
+END { printf "TAC = %d\n",tac; }
+END { printf "TAT = %d\n",tat; }
+END { printf "TAG = %d\n",tag; }
+END { printf "TCA = %d\n",tca; }
+END { printf "TCC = %d\n",tcc; }
+END { printf "TCT = %d\n",tct; }
+END { printf "TCG = %d\n",tcg; }
+END { printf "TTA = %d\n",tta; }
+END { printf "TTC = %d\n",ttc; }
+END { printf "TTT = %d\n",ttt; }
+END { printf "TTG = %d\n",ttg; }
+END { printf "TGA = %d\n",tga; }
+END { printf "TGC = %d\n",tgc; }
+END { printf "TGT = %d\n",tgt; }
+END { printf "TGG = %d\n",tgg; }
+END { printf "GAA = %d\n",gaa; }
+END { printf "GAC = %d\n",gac; }
+END { printf "GAT = %d\n",gat; }
+END { printf "GAG = %d\n",gag; }
+END { printf "GCA = %d\n",gca; }
+END { printf "GCC = %d\n",gcc; }
+END { printf "GCT = %d\n",gct; }
+END { printf "GCG = %d\n",gcg; }
+END { printf "GTA = %d\n",gta; }
+END { printf "GTC = %d\n",gtc; }
+END { printf "GTT = %d\n",gtt; }
+END { printf "GTG = %d\n",gtg; }
+END { printf "GGA = %d\n",gga; }
+END { printf "GGC = %d\n",ggc; }
+END { printf "GGT = %d\n",ggt; }
+END { printf "GGG = %d\n",ggg; }