kSpider 2 DBRetina test

annotations.txt

parent	metadata
p1	DB_A
p2	DB_B
p3	DB_C
p4	DB_A
p5	DB_A
p6	DB_A
p7	DB_B
p8	DB_C
p9	DB_C

names.tsv

requirements.txt

DBRetina

test.ipynb

{
 "cells": [
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   "cell_type": "code",
   "execution_count": 1,
   "id": "alert-vinyl",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ID\tseq1\tseq2\tshared_kmers\n",
      "1\t7\t2\t1\n",
      "2\t6\t1\t1\n",
      "3\t8\t3\t1\n",
      "4\t5\t1\t1\n",
      "5\t6\t4\t1\n",
      "6\t5\t4\t1\n",
      "7\t6\t5\t1\n",
      "8\t9\t3\t1\n",
      "9\t9\t8\t1\n",
      "10\t4\t1\t1\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "DBRetina items_indexing -i annotations.txt -n names.tsv -p tmp\n",
    "DBRetina pairwise -i tmp\n",
    "cat tmp_kSpider_pairwise.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "lyric-opening",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ID\tseq1\tseq2\tshared_kmers\n",
      "1\t7\t2\t1\n",
      "2\t6\t1\t1\n",
      "3\t8\t3\t1\n",
      "4\t5\t1\t1\n",
      "5\t6\t4\t1\n",
      "6\t5\t4\t1\n",
      "7\t6\t5\t1\n",
      "8\t9\t3\t1\n",
      "9\t9\t8\t1\n",
      "10\t4\t1\t1\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cat tmp_kSpider_pairwise.tsv"
   ]
  }
 ],
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