notebooks/trimming_example.ipynb

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   "source": [
    "import gzip\n",
    "from pathlib import Path\n",
    "\n",
    "from tqdm.notebook import tqdm\n",
    "\n",
    "import hits.fastq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "9ad7e8c1-18a6-4d08-88e7-d289a5160ed5",
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   "source": [
    "base_dir = Path('/lab/solexa_weissman/jah/projects/dCas9_fusions')"
   ]
  },
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   "cell_type": "code",
   "execution_count": 3,
   "id": "81b23d4d-27ac-4201-b54c-8d1826c68eec",
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   "source": [
    "batches = [\n",
    "    '220527_pL1_pL2',\n",
    "    '220610_pL1_pL2',\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "5234e9de-3e7b-4e2a-8d09-299f5fa5560c",
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    {
     "data": {
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       "model_id": "a4f3bffc553a423292ca32430a3953b9",
       "version_major": 2,
       "version_minor": 0
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       "0it [00:00, ?it/s]"
      ]
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   ],
   "source": [
    "for batch in batches:\n",
    "    data_dir = base_dir / 'data' / batch\n",
    "    \n",
    "    for fn_name in ['pL1', 'pL2']:\n",
    "        fn = (data_dir / fn_name).with_suffix('.fastq.gz')\n",
    "        trimmed_fn = (data_dir / (fn_name + '_trimmed')).with_suffix('.fastq.gz')\n",
    "        \n",
    "        with gzip.open(trimmed_fn, 'wt', compresslevel=1) as fh: \n",
    "            for read in progress(hits.fastq.reads(fn)):\n",
    "                fh.write(str(read[16:-16]))"
   ]
  }
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