{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "510d6b2b-4f0d-4dfa-95de-d9ca49758149",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "898a88c1-ab71-4a18-8362-c907fb28edce",
   "metadata": {},
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       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38205_38250.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38250_38295.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38295_38340.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38340_38385.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38385_38430.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38430_38475.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38475_38520.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38520_38565.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38565_38610.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38610_38655.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38655_38700.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38700_38745.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38745_38790.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38790_38835.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38835_38880.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38880_38925.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38925_38970.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_38970_39015.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39015_39060.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39060_39105.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39105_39150.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39150_39195.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39195_39240.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39240_39285.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39285_39330.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39330_39375.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39375_39420.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39420_39465.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39465_39510.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39510_39555.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39555_39600.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39600_39645.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39645_39690.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39690_39735.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39735_39780.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39780_39825.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39825_39870.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39870_39915.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39915_39960.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_39960_40005.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40005_40050.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40050_40095.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40095_40140.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40140_40185.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40185_40230.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40230_40275.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40275_40320.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40320_40365.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40365_40410.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40410_40455.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40455_40500.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40500_40545.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40545_40590.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40590_40635.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40635_40680.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40680_40725.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40725_40770.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40770_40815.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40815_40860.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40860_40905.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40905_40950.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40950_40995.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_40995_41040.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41040_41085.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41085_41130.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41130_41175.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41175_41220.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41220_41265.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41265_41310.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41310_41355.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41355_41400.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41400_41445.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41445_41490.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41490_41535.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41535_41580.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41580_41625.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41625_41670.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41670_41715.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41715_41760.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41760_41805.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41805_41850.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41850_41895.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41895_41940.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41940_41985.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_41985_42030.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42030_42075.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42075_42120.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42120_42165.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42165_42210.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42210_42255.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42255_42300.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42300_42345.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42345_42390.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42390_42435.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42435_42480.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42480_42525.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42525_42570.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42570_42615.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42615_42660.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42660_42705.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42705_42750.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42750_42795.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42795_42840.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42840_42885.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42885_42930.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42930_42975.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_42975_43020.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43020_43065.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43065_43110.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43110_43155.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43155_43200.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43200_43245.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43245_43290.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43290_43335.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43335_43380.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43380_43425.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43425_43470.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43470_43515.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43515_43560.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43560_43605.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43605_43650.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43650_43695.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43695_43740.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43740_43785.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43785_43830.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43830_43875.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43875_43920.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43920_43965.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_43965_44010.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44010_44055.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44055_44100.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44100_44145.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44145_44190.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44190_44235.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44235_44280.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44280_44325.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44325_44370.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44370_44415.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44415_44460.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44460_44505.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44505_44550.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44550_44595.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44595_44640.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44640_44685.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44685_44730.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44730_44775.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44775_44820.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44820_44865.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44865_44910.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44910_44955.npy'),\n",
       " PosixPath('jobs/ncRNA_dataset2/output/sequences_ncRNA_dataset2_44955_45000.npy'),\n",
       " ...]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# src_dir = Path(\"jobs/FLIP_human/\")\n",
    "# src_dir = Path(\"jobs/FLIP_mixed/\")\n",
    "src_dir = Path(\"jobs/ncRNA_dataset2/\")\n",
    "dataset_name = src_dir.stem\n",
    "src_files = list(src_dir.glob(\"output/*.npy\"))\n",
    "src_files = sorted(src_files, key=lambda p: (len(str(p)), str(p)))\n",
    "src_files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "745cdab1-6b99-48a7-8078-03182102643d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(45447, 45447)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "blocks = [np.load(file) for file in src_files]\n",
    "# lcs_matrix_ur = np.vstack([b[:437] for b in blocks])\n",
    "lcs_matrix_ur = np.vstack(blocks)\n",
    "lcs_matrix_ur.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "b78390cb-e8b5-4725-8f68-94e4d3d36a03",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[123,  54,  91, ...,  65,  73,  89],\n",
       "       [  0,  74,  59, ...,  52,  59,  63],\n",
       "       [  0,   0, 186, ...,  77,  79, 104],\n",
       "       ...,\n",
       "       [  0,   0,   0, ...,  97,  63,  74],\n",
       "       [  0,   0,   0, ...,   0, 108,  82],\n",
       "       [  0,   0,   0, ...,   0,   0, 156]])"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lcs_matrix_ur"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "66060906-424b-4541-9d8b-13cc4da2a640",
   "metadata": {},
   "outputs": [],
   "source": [
    "lcs_matrix = lcs_matrix_ur + (lcs_matrix_ur.T * (1-np.eye(lcs_matrix_ur.shape[0])))\n",
    "lcs_matrix = lcs_matrix.astype(\"uint16\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "5887f6c1-26bc-4268-8950-c9f75054f3c8",
   "metadata": {},
   "outputs": [],
   "source": [
    "np.save(f\"lcs_{dataset_name}.npy\", lcs_matrix, allow_pickle=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4f01c27c-62da-4bab-9f47-62db8fe8aa0c",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.7"
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