{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d3dfbcc5",
   "metadata": {},
   "outputs": [],
   "source": [
    "%cd ~/projects/cmdb-quantbio/assignments/bootcamp/dictionaries_file_io/"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5de1e054",
   "metadata": {},
   "source": [
    "- Open a filestream for the file \"CDS.fa\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e694b5c2",
   "metadata": {},
   "outputs": [],
   "source": [
    "fa_fname = \"actin.fa\"\n",
    "fs = open(fa_fname)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cefb411d",
   "metadata": {},
   "source": [
    "- Create a list to hold the sequence being read in\n",
    "- Use a for loop to read the file, line by line\n",
    "- Capture the sequence name with a conditional\n",
    "- Before adding each sequence line to the list, remove any newline or space characters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c3b10cb8",
   "metadata": {},
   "outputs": [],
   "source": [
    "sequence = []\n",
    "for line in fs:\n",
    "    if line.startswith('>'):\n",
    "        name = line.rstrip().lstrip('> ')\n",
    "        continue\n",
    "    sequence.append(line.rstrip())\n",
    "fs.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2580a9f4",
   "metadata": {},
   "source": [
    "- Concatenate the list of sequences into a single sequence string"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "03306c81",
   "metadata": {},
   "outputs": [],
   "source": [
    "sequence = ''.join(sequence)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "10fdf061",
   "metadata": {},
   "source": [
    "- Open a filestream to the codon table file\n",
    "- Create a dictionary to hold the codon/amino acid pairs\n",
    "- Read in the file, line by line\n",
    "- Strip newline and space characters from line and split by tabs to create a list of key and value\n",
    "- Add the key/value pair to the dictionary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "073176bb",
   "metadata": {},
   "outputs": [],
   "source": [
    "codon_fname = \"codons.tsv\"\n",
    "codons = {}\n",
    "for line in open(codon_fname):\n",
    "    codon, aa = line.rstrip().split('\\t')\n",
    "    codons[codon] = aa"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "04765a58",
   "metadata": {},
   "source": [
    "- Create a list to hold the translated sequence\n",
    "- For each codon, look up its corresponding amino acid and add it to the amino acid list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4e053af4",
   "metadata": {},
   "outputs": [],
   "source": [
    "AAs = []\n",
    "for i in range(0, len(sequence), 3):\n",
    "    AAs.append(codons.get(sequence[i:i+3], ' '))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c190bc96",
   "metadata": {},
   "source": [
    "- Open a filestream to write the results to\n",
    "- Write the sequence name with the greater than symbol (fasta format) (don't forget the newline character)\n",
    "- Join the amino acid letters to create an output line and write it to the file (don't forget the newline character)\n",
    "- Close the output filestream"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "49cb1fca",
   "metadata": {},
   "outputs": [],
   "source": [
    "out_fname = \"amino_acids.fa\"\n",
    "output = open(out_fname, 'w')\n",
    "output.write(f\">{name}\\n\")\n",
    "# output.write(''.join(AAs))\n",
    "for i in range(0, len(AAs), 40):\n",
    "    output.write(''.join(AAs[i:i+40]) + '\\n')\n",
    "output.close()"
   ]
  }
 ],
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