Gene Structure

genome.txt

GCAAAGGCTCACCCAAGGCTCCGAATCACACTATCTGAGCAACATTTCAAGACACTCTGCAACACCACGCCAGCCTCGGAAAAGCGTGCAAATCTGCTGTGAAGATGCTCAGGCCTTCATTGCCAAAGACTCTGACGGCTTTTGGCCCGCCTTAACCAGCTGGGTGGCCGGCCCGGACAGTGCCCGTCGCGGATCTCTGCATGGCTTCAAACCAGAAAGGTGCTCTCAACGTCGGGCAACAGTGAGGTATGCGACTCCCCTTGCATCACATGGACTTGTCCTGGGAGGCCTTTTCTTGGGCCGTTCATTGCGGAGATGTCGGCAAGGTTCTCTGCAAGACCGTGTCAGCCACGGCCCTTGCGAGGCTGAGTTGAGGTCTGGCTATCTGTCTCGAGATGGACCTCACTGGGTCGTCATGGCTGGCTCGAGGCCTTGCTGGCTGGGCCTTTGCCTGGAGCTTCATGATATTGCCAAGCCTCGGAGCTCCCTTCGAATTGGTCAAGTGGTCTGCTTGGCTCGCCGTACCCAAGGTTACCCCAAGGTACCTACCTACCTACCTACACTAACCTACCTACCCTCCCTCTGCGGAGGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATCAGCAACAGCGACAAATCAGCACACACGGCAAGCAAAGCACCCACGGGAGCTGGCTGTTAGCTGACTGAGCTCGAGCTTCCATCCCTTCGCTTAGCTTGGACGTCGGCACCTTCCCTCCTGTACGGACGCATGTCTCAGGCGCGGTTGCGCTCAAACACGGCGGGCAATCACCTGGAAGGACACAACATCAAAGGGCCCATCAGTGGCATGCATCTTCGGCCCTTCTGAATTTTCGAGCGTCTCCTGGCGCCAACTTCAACACCAAACCTCGTCGCGATCATCCTTCCGGCCAAAACACCACTTTTCCATCCGCCAACCCCGCTTCATCCACTTCCACCAGTTCCACGCAAATCCCGCGCCGTTGCCCCGTCAATATCAACATCCAGCATCGTCACGACCACCGGTTTTATTCTCGACACTACGTCCATCCGCCCATCCCGCGCACAACCATCCCACCCCGTTCAATCCCTTCAAACAAACAAACAAACACAATGGCTGGCGGAAAGGGCAAGTCGTCTGGCGGCAAGAGCTCGGGTGGAAAGACCTCGGGCGTCGAAGGTCCCAAGAAGCAGCAGAGCCATTCTGCTCGCGCTGGTCTTCAGGTACGTTTTTATAGTTGACGAGCTTCATGGCTCTGTCCGCTTTCAATTCCTGCTCCGATCTGCACCATCGACGTCGTCTCATCAACCAACTTTTTTTTTGCTCGCATCCGCCATCCCTGTCGTCAGATGTCGATGGAATCACGCCGATACACCACAACGCGTCCACCGAGCCCCCTACATTTCCGGACAACCCCATAGTGCCAACCTACGAAGAACGCGAACTCGCTGCCTCACACGTCGGTCGCACACAACCCCGCCGCTGGGTAAAAGAAAAAAACCCCCATTGCGCCCCGTACGCGATACTATTTCGGCTTCATATGGACGCGTTGTTCTGTGCATCCTTCTCTCGCCCTGGCCCCGCACCCGGACCTTGTTCCGGTCCCTAACTTTGGATTTCTCGCTCTGACAACGAGGCGGAGCTGCGGCGTGCATTTCCGTCCTCTGGAGTTTGCCGTGTGTCTGATGCGCCATGCTGACTTGAATCTAATTAGTTCCCTTGCGGTCGTGTCAAGCGTTTCCTGAAGCAGAACACCCAAAACAAGATGCGCGTTGGCGCCAAGGCTGCCGTCTATGTTACTGCCGTGCTGGAATATTTGACTGCTGAAGTCCTCGAACTTGCGGGTGTAAGTCATTCATACCCCATCCGCTCGGCCATATTGCTTGGCGACGAGGAGGCTCCCATTTCCAAGTTTTACCTGCTTTATGGCTAACTCAATGATTTCCGTTGTATAGAACGCTGCCAAGGACCTGAAGGTCAAGCGTATTACTCCCCGCCATCTTCAGCTTGCCATCCGTGGAGATGAGGAGCTTGATACCCTCATCCGCGCCACTATCGCCTTCGGTGGTGTCCTCCCCCACATTAACCGCGCCCTTCTGCTCAAGGTAGAGCAGAAGAAGAAGGCCAAGGCTCAGGAGGCTTAAGTCCACAACTGCACCGAAAAACTCGACGTCGCACACGTTTCGCACACTGTCTTGCATCTCTCTAGCCCCGCTCCGGGCTGACGGGCAGGACAGCAATCGGCTTGTTCAAGGGATGTCACGGGGTGATGCCGGGGGGGTTGGGGATTGTCTTCGCTAATCCAACACTAACGCCGCTGTATTGTTGGGTATTTTCTTCCTATTATTTGTTGTTGGGATACGCACACGGGCTTGGGGCCCACCGAACCATGGCTTGAAAAAGCCGAGCACTCCCGGTGTCTGCGACGGCAACAAGCGCAGCGCATAGACGACGGCGAACTTCCCTTGCGACACTTCCAGCAGAGTGGTGCGTTCGGAACACACACGAAAAGCGAAGCGTTCTGTATCATCCAGACGTGGAAGCCGCTTGGGTGGCGATGAGCAGGGAGACCATTCACTGTATAATGTCATCTTGGAGTGCACCACACACTGGGAACGGCGAGCAATCTCCCCTCGTCACGGCGCGGCGTGCGACAGCAGCTCTTTTACGATATCTGTAACAACATGAATCTTCTTTATCGTTTTTTTTATAGTACGACTCGGCCATGAGGGCTTAGCGAGGAAAACATCAGGACACGTTAAATGAACGTGTCGGTTGGTACTGGTTGCAGGTAGTGGCGGAATAAAGGCTACAAGGAAGAGCCTTGAAAATTTGCGATACCAATTCTTATTATGTTCTCTCTACAGTCTGGGATGCGCAATTCTATTCATGGTGACTACAATGTGTTCAGTCTCACCATCTGCTGTTTCGGACGACACTGATACCCGCTGCCGATTACTACATGAGAAAACGCAGGTAAGGTAGATCCAAGTATTGTTGTCATTCTAGAAGCTAACTTGGTGAACTCTCTTTAAGCAAGACCTCTATGCCCTACCGATCCATGACCATGGAGTTTTCGTACCTATAACAAGACGATATGTGTCATTCAGAGCTTTGATCCTCTACCTTTCAAGGTTTTTACTTCCCGGACAATTGATCACGTTTGCATGGCCACATCATTCTCCATAGGCCCGAATTAAATGAATGAGGCAAACGACTCGTAAATGTCCGGGTTAGCGATTCCCACAGCGAGACGGCCTCCAGCCAAGGGCGACACCGGCGAAACTGAAATGGTCTCCAGATCGTCCTTCAACAGCTTCGCAGGATCAATAGTCATCTCATCCGCAACCATGGTAATGTAACAGTCCTGGCGAGAACTGCAGCCGTCCAGCCTAGAATAGGGCTCAAGCGCGGCAACCGTGAGGTTGCCGGTGTTGTCATCCTCCGGGTCCTTCTGCGTCCCTTGTGCTGCTATCATGGTCTCCTTCCAATCGAACTTGATAGTCGCCTCCTTGACAAGCAACTGTTCATCTTCCGAACCCGAGGCGTCTGAAGAAGAGCTACTGCTGCCACCAGCAGAGGAGGTCGACGATGACGAAGAAGAGTCATCACTTTTTTTCTCCCCGACACTCCCACTCCCATTTCCCTCGTGTCCCCTTCCCTTCCTCCCACTACTTCTCTGTCCACCCATCCTCCTCTCCCTTTCTTCCTGTCCACTCCTACTCCTCCTCGCTCCCAACGCCTTCTTCATAGTCTCCCTCTCCCTCTCCCTTTCCTTACGCCTCTGAGCCTCGATGGCGTCCTTATCCCTATCATTCACCCACACCAATTTCTTGGCATTCCTGTCAATCTTAGCACGACCTTCTTCGCACGCAGCGATGACAGTCTGTCGACACTCGGACGGGTAGTCGCAGTGAGACCAGCAGTTGTGGGTGCGTTCGACGTACATCTTTTCTTTGGCCCGGGCGATGGAGCGGGTCTCGCGCTCAGAGACGTGATGCCAGGCTAGGGTTGTAGCTCTAGGCGATTTTGAGCCTGGGCCTGGGGGTGAAGATGAAGACGAACTTGAAGATGAGTCTAAGGGGGGGACGGGGATGAGATGCCATGTTGCAAAGTCTTGGAGGCGAGCGGCGGCGACTTTGTCATTGGCAGATTGGGATGAGTCCGAGTCAGAGGTGGTGGTGGTATCTTTTCTATTAGAGCTGGAAGAAAGGGAGGGACGAGGAGAGAGAGAAACACTGGTGAGTCTCCTCTTCCCACTCGATCCCAACTTCTTCTTTCCACTATCATCATCATCATCATCATCATCATCATCACCACCACCACCAACTGTCAAAGCACGCCTGGCAGCAGCACCCGTCACACTCCGTCGAAAGCTTCCCCACGCCGACCAACCCAAGTAATCAAACTCGGCGGTGCACGGTCCTCCTCCTTTTCTGCCACTTCCGCTTCGCTTTCTTTTCTTTCCAGTCTTGTCTCTCTCTTCAGATTCCCTTTGATTAATGGCAGGCATTAAACAGCAAAAGACATGTCCACACTCCAGGCATCTCCTCGTGCAGGCTAGCCGGTATACAGACCGGCAGGAGTGGCAGGACCACAGCCAGGGGTAGGGAGCGGGAGGCGAGAGCATGGGCGGCGTTGTTGGTGGTGTTGGAGACTTTTGGGTATTGCTGCTTGATGACGTACTTCTGTTGGTAATTGGACTTGTGGGTGACGGCTGAGTTGGTGAAAATTTGGCTGTGTTTTTGTTGTCGGTGGTGGTGGTGCCACTACCATCAAAAGTATCAGCGATGGGCGAGTTGGGACTGTTTTGAGGCTTGACTTTTGTGGGGGAGTTGATCATCTCTGAGATAGAGCCGGTGACAATGGTTAGCTCTGGGATGATGTCGAAGAGGACGAGCCTGGGTGGCTTTGCCTTTGCATTAGGTGTTGAGGGCATCTTGTTTGGACTGTTGTGTGTCCTTGTTGAGTTG

identify.py

from pprint import pprint
from dataclasses import dataclass
from enum import Enum, auto
from time import sleep

from rich import print
from rich.text import Text
from rich.style import Style
from rich.console import Console

class Role(Enum):
    untranslated = auto()
    start_codon = auto()
    stop_codon = auto()
    intron = auto()
    for_translation = auto()

class Mode(Enum):
    not_translating = auto()
    excluding_intron= auto()
    reading = auto()
    
@dataclass
class Region:
    dna: str
    role: Role

    def styled_text(self) -> Text:
        text = Text(self.dna)
        
        if self.role == Role.start_codon:
            text.stylize(style=Style(bgcolor="green"), start=0, end=len(self.dna))
        elif self.role == Role.stop_codon:
            text.stylize(style=Style(bgcolor="red"), start=0, end=len(self.dna))
        elif self.role == Role.intron:
            text.stylize(style="underline", start=0, end=len(self.dna))
        elif self.role == Role.untranslated:
            text.stylize(style="italic", start=0, end=len(self.dna))
        
        return text


with open('genome.txt') as f:
    dna = f.read()

regions = []
buffer = []

def got_start_codon(codon):
    global buffer, mode
    previous = ''.join(buffer[:-3])
    match mode:
        case Mode.not_translating:
            role = Role.untranslated
        case Mode.excluding_intron:
            role = Role.intron
        case Mode.reading:
            return
            
    regions.extend([Region(previous, role), Region(codon, Role.start_codon)])
    buffer = []
    mode = Mode.reading

def got_stop_codon(codon):
    global buffer, mode
    previous = ''.join(buffer[:-3])
    if mode == Mode.reading:
        regions.extend([Region(previous, Role.for_translation), Region(codon, Role.stop_codon)])
        buffer = []
        mode = Mode.excluding_intron

# start not translating
mode = Mode.not_translating

for nucleotide in dna:
    buffer.append(nucleotide)
    if len(buffer) > 3:
        last3 = ''.join(buffer[-3:])
        match last3:
            case 'ATG': # start codon
                got_start_codon(last3)
            case 'TAA' | 'TAG' | 'TGA': # end codon
                got_stop_codon(last3)

# unless the sequence terminated with a codon, 
# mark the remainder as untranslated
if buffer:
    regions.append(Region(''.join(buffer), Role.untranslated))
                    
console = Console()

# print with the start codons at the beginning of the lines
for region in regions:
    if region.role in [Role.start_codon, Role.for_translation]:
        console.print(region.styled_text(), end='')
    else:
        console.print(region.styled_text())
        sleep(0.15)  # just so the asciicast can see it all


# Create a Console instance to record content for HTML export
html_console = Console(force_terminal=True, record=True)

for region in regions:
    if region.role in [Role.start_codon, Role.for_translation]:
        html_console.print(region.styled_text(), end='')
    else:
        html_console.print(region.styled_text(), end='\n')

# Save the recorded content to an HTML file
with open("genome.html", "wt") as html_file:
    html_file.write(html_console.export_html())

video.md

https://asciinema.org/a/4y4kmn1jmsvhXbxaxMUxYqsGI