Simple example of how to calculate coverage per position of a multiple sequence alignment

calculate_coverage_per_position.py.ipynb

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   "source": [
    "import Bio.AlignIO\n",
    "from matplotlib import pyplot as plt\n",
    "import re"
   ]
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    "alignment_path = \"builds/loes-2024/ha/aligned.fasta\""
   ]
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   "source": [
    "alignment = Bio.AlignIO.read(alignment_path, \"fasta\")"
   ]
  },
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   "source": [
    "number_of_records = len(alignment)"
   ]
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   "source": [
    "coverages = []\n",
    "for position in range(alignment.get_alignment_length()):\n",
    "    coverage = len(re.findall(r\"[ACGT]\", alignment[:, position]))\n",
    "    coverages.append(coverage)"
   ]
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   "source": [
    "fig, ax = plt.subplots(1, 1, figsize=(8, 4), dpi=300)\n",
    "ax.plot(\n",
    "    coverages,\n",
    ")\n",
    "\n",
    "ax.set_ylim(bottom=0)\n",
    "\n",
    "ax.set_xlabel(\"Alignment position\")\n",
    "ax.set_ylabel(\"Number of records\")"
   ]
  }
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