PandasLab.ipynb

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    "## Pandas Lab 1\n",
    "For this lab, you will need to read in the provided FASTA file and generate a DataFrame containing the following information for each sequence record:\n",
    "1. Sequence Length\n",
    "2. GC content\n",
    "3. Begins with start codon?\n",
    "4. Ends in stop codon?\n",
    "5. Complete frame? (Meaning is the length a multiple of 3?)\n",
    "\n",
    "The row index should be the sequence label, and columns should be labeled with descriptions of these 5 criteria I've given you. Be mindful of the datatype you choose for description 3-5."
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    "import pandas as pd\n",
    "\n",
    "#function to find GC content\n",
    "def GC_content(sequence): #produces the proportion of the sequence that is G and C base pairs\n",
    "    GC_count = 0\n",
    "    for base in sequence:\n",
    "        if base == \"G\" or base == \"C\":\n",
    "            GC_count += 1\n",
    "        else:\n",
    "            continue\n",
    "    proportionGC = round(GC_count/len(sequence),3)\n",
    "    return proportionGC\n",
    "\n",
    "#function to return all data needed for data frame\n",
    "def pandas_lists(filename):\n",
    "    #open the file and parse through it to get the header and sequence lines\n",
    "    with open(filename) as fh:\n",
    "        header = None\n",
    "        seq = \"\"\n",
    "        all_seqs = {}\n",
    "        for line in fh:\n",
    "            line = line.rstrip()\n",
    "            if line.startswith(\">\"):\n",
    "                if header:\n",
    "                    all_seqs[header] = seq\n",
    "                header = line\n",
    "                seq = \"\"\n",
    "            else:\n",
    "                seq += line\n",
    "        if header:\n",
    "            all_seqs[header] = seq\n",
    "    \n",
    "    #initialize empty lists that will be returned\n",
    "    sequence_labels = []\n",
    "    data = []\n",
    "    \n",
    "    #parse through the dictionary created above\n",
    "    for header,seq in all_seqs.items():\n",
    "        #initialize list for just this sequence iteration\n",
    "        seq_data = []\n",
    "        \n",
    "        #find the sequence label for this iteration\n",
    "        header = header.split()\n",
    "        label = header[0].lstrip(\">\")\n",
    "        sequence_labels.append(label)\n",
    "        \n",
    "        #find the sequence length for this iteration\n",
    "        length = len(seq)\n",
    "        seq_data.append(length)\n",
    "        \n",
    "        #find the GC conent for this iteration using the GC function\n",
    "        gc = GC_content(seq) \n",
    "        seq_data.append(gc)\n",
    "        \n",
    "        #find if the sequence starts with a start codon\n",
    "        #start codon is ATG\n",
    "        if seq[:3] == \"ATG\":\n",
    "            seq_data.append(True)\n",
    "        else:\n",
    "            seq_data.append(False)\n",
    "            \n",
    "        #find if the sequence ends with a stop codon\n",
    "        #stop codons are TAA, TAG and TGA\n",
    "        if seq[length-3:] == \"TAA\":\n",
    "            seq_data.append(True)\n",
    "        elif seq[length-3:] == \"TAG\":\n",
    "            seq_data.append(True)\n",
    "        elif seq[length-3:] == \"TGA\":\n",
    "            seq_data.append(True)\n",
    "        else:\n",
    "            seq_data.append(False)\n",
    "        \n",
    "        #find if the sequence is a complete frame\n",
    "        #it is complete if it divides evenly by three\n",
    "        frame = length % 3\n",
    "        if frame == 0:\n",
    "            seq_data.append(True)\n",
    "        else:\n",
    "            seq_data.append(False)\n",
    "        \n",
    "        #add the data from the iteration to the larger data list\n",
    "        data.append(seq_data)\n",
    "        \n",
    "    #return the lists of labels and of data    \n",
    "    return sequence_labels,data\n",
    "        "
   ]
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       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Sequence Length</th>\n",
       "      <th>GC%</th>\n",
       "      <th>Valid Start</th>\n",
       "      <th>Valid Stop</th>\n",
       "      <th>Complete Frame</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>MD10G1276500</th>\n",
       "      <td>2940</td>\n",
       "      <td>0.461</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD10G1110200</th>\n",
       "      <td>1731</td>\n",
       "      <td>0.464</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD10G1036500</th>\n",
       "      <td>468</td>\n",
       "      <td>0.545</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD10G1170700</th>\n",
       "      <td>1728</td>\n",
       "      <td>0.447</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD10G1250900</th>\n",
       "      <td>1278</td>\n",
       "      <td>0.403</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD14G1066400</th>\n",
       "      <td>423</td>\n",
       "      <td>0.530</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD14G1225900</th>\n",
       "      <td>594</td>\n",
       "      <td>0.503</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD14G1120900</th>\n",
       "      <td>939</td>\n",
       "      <td>0.481</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD14G1057700</th>\n",
       "      <td>483</td>\n",
       "      <td>0.524</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MD14G1237500</th>\n",
       "      <td>3270</td>\n",
       "      <td>0.442</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7496 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              Sequence Length    GC%  Valid Start  Valid Stop  Complete Frame\n",
       "MD10G1276500             2940  0.461        False        True            True\n",
       "MD10G1110200             1731  0.464         True        True            True\n",
       "MD10G1036500              468  0.545         True        True            True\n",
       "MD10G1170700             1728  0.447         True        True            True\n",
       "MD10G1250900             1278  0.403         True        True            True\n",
       "...                       ...    ...          ...         ...             ...\n",
       "MD14G1066400              423  0.530         True        True            True\n",
       "MD14G1225900              594  0.503         True        True            True\n",
       "MD14G1120900              939  0.481         True        True            True\n",
       "MD14G1057700              483  0.524         True        True            True\n",
       "MD14G1237500             3270  0.442         True        True            True\n",
       "\n",
       "[7496 rows x 5 columns]"
      ]
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   "source": [
    "lists = pandas_lists(\"Mdomestica-pandasLab.fa\")\n",
    "sequence_labels = lists[0]\n",
    "data = lists[1]\n",
    "\n",
    "df = pd.DataFrame(data, index=sequence_labels, columns=[\"Sequence Length\", \"GC%\", \"Valid Start\", \"Valid Stop\", \"Complete Frame\"])\n",
    "df                \n",
    "\n",
    "#this worked and gave the intended table with sequence labels and correct columns\n",
    "# a \"True\" in the \"Valid Start\" column means the sequence begins with a start codon, \"False\" means it does not\n",
    "# a \"True\" in the \"Valid Stop\" column means the sequence ends with a stop codon, \"False\" means it does not\n",
    "# a \"True\" in the \"Complete Frame\" column means the sequence is a mulitple of 3, \"False\"  means it is not\n",
    "\n",
    "# Sequence Length\tGC%\tValid Start\tValid Stop\tComplete Frame\n",
    "# MD10G1276500\t2940\t0.461\tFalse\tTrue\tTrue\n",
    "# MD10G1110200\t1731\t0.464\tTrue\tTrue\tTrue\n",
    "# MD10G1036500\t468\t0.545\tTrue\tTrue\tTrue\n",
    "# MD10G1170700\t1728\t0.447\tTrue\tTrue\tTrue\n",
    "# MD10G1250900\t1278\t0.403\tTrue\tTrue\tTrue\n",
    "# ...\t...\t...\t...\t...\t...\n",
    "# MD14G1066400\t423\t0.530\tTrue\tTrue\tTrue\n",
    "# MD14G1225900\t594\t0.503\tTrue\tTrue\tTrue\n",
    "# MD14G1120900\t939\t0.481\tTrue\tTrue\tTrue\n",
    "# MD14G1057700\t483\t0.524\tTrue\tTrue\tTrue\n",
    "# MD14G1237500\t3270\t0.442\tTrue\tTrue\tTrue\n",
    "# 7496 rows × 5 columns"
   ]
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