usecases/compute_absolute_enrichment.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "from pathlib import Path\n",
    "import logging\n",
    "import toml\n",
    "import copy\n",
    "\n",
    "from simreaduntil.shared_utils.logging_utils import add_comprehensive_stream_handler_to_logger, setup_logger_simple\n",
    "from simreaduntil.seqsum_tools.seqsum_plotting import preprocess_seqsum_df_for_plotting\n",
    "\n",
    "\n",
    "add_comprehensive_stream_handler_to_logger(None)\n",
    "logging.getLogger(__name__).setLevel(logging.DEBUG)\n",
    "logging.getLogger(\"simreaduntil\").setLevel(logging.DEBUG)\n",
    "\n",
    "logger = logging\n",
    "\n",
    "# logging.getLogger(None).setLevel(logging.ERROR)\n",
    "# logging.getLogger(\"simreaduntil\").setLevel(logging.ERROR)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "# run_dir = Path(\"/home/mmordig/ont_project_all/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_withflanking/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_realmapper_accel5/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_fakemapper_accel10/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_realmapper_withunaligned_constantgapsampler_accel5/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_realmapper_withunaligned_accel10/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_realmapper_withunaligned_accel5/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_realmapper_withunaligned_accel2/simulator_run/\")\n",
    "# run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_realmapper_withunaligned_accel3_longer/simulator_run/\")\n",
    "run_dir = Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_realreads_realmapper_withunaligned_accel5_longer/simulator_run/\")\n",
    "\n",
    "seqsum_filename = run_dir / \"sequencing_summary.txt\"\n",
    "sim_config = {\"readfish_config_file\": run_dir / \"..\" / \"configs/readfish_enrich_per_quadrant.toml\" }\n",
    "\n",
    "readfish_conditions = [v for v in toml.load(sim_config[\"readfish_config_file\"])[\"conditions\"].values() if isinstance(v, dict)]\n",
    "channel_assignments_toml = run_dir / \"channels.toml\"\n",
    "channel_assignments_per_cond = toml.load(channel_assignments_toml)\n",
    "channels_per_condition = {condition_dict[\"name\"]: condition_dict[\"channels\"] for condition_dict in channel_assignments_per_cond[\"conditions\"].values()}\n",
    "\n",
    "logger.debug(f\"Reading sequencing summary file '{seqsum_filename}'\")\n",
    "full_seqsum_df = pd.read_csv(seqsum_filename, sep=\"\\t\")#, nrows=100) # todo\n",
    "logger.debug(f\"Done reading sequencing summary file '{seqsum_filename}'\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# partial_seqsum_df.columns\n",
    "# full_seqsum_df[\"channel\"].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2024-03-01 10:33:16,409 - Sorting and cleaning seqsummary file of shape (184996, 13) --- seqsum_plotting.py:939 (preprocess_seqsum_df_for_plotting) INFO ##\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing condition control\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2024-03-01 10:33:16,677 - Adding previous gap duration to seqsummary --- seqsum_plotting.py:941 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:16,835 - Adding group column from NanoSim read id --- seqsum_plotting.py:951 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:17,431 - Splitting according to groups {'enrich_chr_1_8': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8'], 'enrich_chr_9_14': ['chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14'], 'enrich_chr_16_20': ['chr16', 'chr17', 'chr18', 'chr19', 'chr20'], 'other': {'chr21', 'chrY', 'chr15', 'chr22', 'chrX'}} --- seqsum_plotting.py:964 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:17,453 - Adding extra columns for plotting --- seqsum_plotting.py:971 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:17,543 - /tmp/ipykernel_1011868/1748468773.py:16: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.\n",
      "  num_sequenced_bps_per_group = dict(partial_seqsum_df.groupby(\"group\")[\"cum_nb_seq_bps_per_group\"].max())\n",
      " --- warnings.py:109 (_showwarnmsg) WARNING ##\n",
      "2024-03-01 10:33:17,651 - Sorting and cleaning seqsummary file of shape (355109, 13) --- seqsum_plotting.py:939 (preprocess_seqsum_df_for_plotting) INFO ##\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing condition enrich_chr_1_8\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2024-03-01 10:33:18,095 - Adding previous gap duration to seqsummary --- seqsum_plotting.py:941 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:18,389 - Adding group column from NanoSim read id --- seqsum_plotting.py:951 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:19,486 - Splitting according to groups {'enrich_chr_1_8': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8'], 'enrich_chr_9_14': ['chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14'], 'enrich_chr_16_20': ['chr16', 'chr17', 'chr18', 'chr19', 'chr20'], 'other': {'chr21', 'chrY', 'chr15', 'chr22', 'chrX'}} --- seqsum_plotting.py:964 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:19,527 - Adding extra columns for plotting --- seqsum_plotting.py:971 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:19,697 - /tmp/ipykernel_1011868/1748468773.py:16: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.\n",
      "  num_sequenced_bps_per_group = dict(partial_seqsum_df.groupby(\"group\")[\"cum_nb_seq_bps_per_group\"].max())\n",
      " --- warnings.py:109 (_showwarnmsg) WARNING ##\n",
      "2024-03-01 10:33:19,821 - Sorting and cleaning seqsummary file of shape (526237, 13) --- seqsum_plotting.py:939 (preprocess_seqsum_df_for_plotting) INFO ##\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing condition enrich_chr_9_14\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2024-03-01 10:33:20,519 - Adding previous gap duration to seqsummary --- seqsum_plotting.py:941 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:20,981 - Adding group column from NanoSim read id --- seqsum_plotting.py:951 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:22,599 - Splitting according to groups {'enrich_chr_1_8': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8'], 'enrich_chr_9_14': ['chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14'], 'enrich_chr_16_20': ['chr16', 'chr17', 'chr18', 'chr19', 'chr20'], 'other': {'chr21', 'chrY', 'chr15', 'chr22', 'chrX'}} --- seqsum_plotting.py:964 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:22,658 - Adding extra columns for plotting --- seqsum_plotting.py:971 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:22,903 - /tmp/ipykernel_1011868/1748468773.py:16: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.\n",
      "  num_sequenced_bps_per_group = dict(partial_seqsum_df.groupby(\"group\")[\"cum_nb_seq_bps_per_group\"].max())\n",
      " --- warnings.py:109 (_showwarnmsg) WARNING ##\n",
      "2024-03-01 10:33:23,035 - Sorting and cleaning seqsummary file of shape (700614, 13) --- seqsum_plotting.py:939 (preprocess_seqsum_df_for_plotting) INFO ##\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing condition enrich_chr_16_20\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2024-03-01 10:33:23,805 - Adding previous gap duration to seqsummary --- seqsum_plotting.py:941 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:24,419 - Adding group column from NanoSim read id --- seqsum_plotting.py:951 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:26,596 - Splitting according to groups {'enrich_chr_1_8': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8'], 'enrich_chr_9_14': ['chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14'], 'enrich_chr_16_20': ['chr16', 'chr17', 'chr18', 'chr19', 'chr20'], 'other': {'chr21', 'chrY', 'chr15', 'chrM', 'chr22', 'chrX'}} --- seqsum_plotting.py:964 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:26,675 - Adding extra columns for plotting --- seqsum_plotting.py:971 (preprocess_seqsum_df_for_plotting) INFO ##\n",
      "2024-03-01 10:33:27,002 - /tmp/ipykernel_1011868/1748468773.py:16: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.\n",
      "  num_sequenced_bps_per_group = dict(partial_seqsum_df.groupby(\"group\")[\"cum_nb_seq_bps_per_group\"].max())\n",
      " --- warnings.py:109 (_showwarnmsg) WARNING ##\n"
     ]
    }
   ],
   "source": [
    "\n",
    "\n",
    "num_sequenced_bps_per_group_per_condition = {}\n",
    "\n",
    "# targets of conditions are disjoint, so we can group by each of them for each condition (a condition is a selseq strategy applied to a subset of channels)\n",
    "group_to_units = {cond[\"name\"]: cond[\"targets\"] for cond in readfish_conditions if cond[\"name\"] != \"control\"}\n",
    "\n",
    "for condition in readfish_conditions:\n",
    "    condition_name = condition[\"name\"]\n",
    "    print(f\"Processing condition {condition_name}\")\n",
    "    subchannels = channels_per_condition[condition_name]\n",
    "    \n",
    "    partial_seqsum_df = full_seqsum_df[full_seqsum_df[\"channel\"].isin([f\"ch{i}\" for i in subchannels])]\n",
    "    # partial_seqsum_df = full_seqsum_df[full_seqsum_df[\"channel\"].isin([i for i in subchannels])]\n",
    "    \n",
    "    partial_seqsum_df, group_column, chrom_column = preprocess_seqsum_df_for_plotting(partial_seqsum_df, group_to_units=copy.deepcopy(group_to_units))\n",
    "    \n",
    "    num_sequenced_bps_per_group = dict(partial_seqsum_df.groupby(\"group\")[\"cum_nb_seq_bps_per_group\"].max())\n",
    "    num_sequenced_bps_per_group_per_condition[condition_name] = num_sequenced_bps_per_group\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "# when having one condition/target per simulation run\n",
    "\n",
    "# group_to_units = {\n",
    "#     'enrich_chr_1_8': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8'],\n",
    "#     'enrich_chr_9_14': ['chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14'],\n",
    "#     'enrich_chr_16_20': ['chr16', 'chr17', 'chr18', 'chr19', 'chr20'],\n",
    "# }\n",
    "# seqsum_filenames_per_cond = {\n",
    "#     \"control\": Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_fakemapper_control/simulator_run/sequencing_summary.txt\"),\n",
    "#     \"enrich_chr_1_8\": Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_fakemapper_chr1to8/simulator_run/sequencing_summary.txt\"),\n",
    "#     \"enrich_chr_9_14\": Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_fakemapper_chr9to14/simulator_run/sequencing_summary.txt\"),\n",
    "#     \"enrich_chr_16_20\": Path(\"/is/cluster-test/fast/mmordig/ont_project/runs/enrich_usecase/readfish_exp/results_readfishexp_fakemapper_chr16to20/simulator_run/sequencing_summary.txt\"),\n",
    "# }\n",
    "\n",
    "# assert(all(x.exists() for x in seqsum_filenames_per_cond.values()))\n",
    "\n",
    "# num_sequenced_bps_per_group_per_condition = {}\n",
    "# for (condition_name, seqsum_filename) in seqsum_filenames_per_cond.items():\n",
    "#     partial_seqsum_df, group_column = preprocess_seqsum_df_for_plotting(seqsum_filename, group_to_units=copy.deepcopy(group_to_units))\n",
    "    \n",
    "#     num_sequenced_bps_per_group = dict(partial_seqsum_df.groupby(\"group\")[\"cum_nb_seq_bps_per_group\"].max())\n",
    "#     num_sequenced_bps_per_group_per_condition[condition_name] = num_sequenced_bps_per_group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "control             : total: 2.67E+09 (1.0), enrich_chr_16_20: 3.35E+08, enrich_chr_1_8: 1.32E+09, enrich_chr_9_14: 6.60E+08, other: 3.54E+08\n",
      "enrich_chr_1_8      : total: 2.12E+09 (1.26), enrich_chr_16_20: 6.32E+07, enrich_chr_1_8: 1.84E+09, enrich_chr_9_14: 1.33E+08, other: 8.11E+07\n",
      "enrich_chr_9_14     : total: 1.94E+09 (1.38), enrich_chr_16_20: 9.16E+07, enrich_chr_1_8: 3.60E+08, enrich_chr_9_14: 1.35E+09, other: 1.36E+08\n",
      "enrich_chr_16_20    : total: 1.75E+09 (1.53), enrich_chr_16_20: 9.05E+08, enrich_chr_1_8: 4.61E+08, enrich_chr_9_14: 2.40E+08, other: 1.43E+08\n"
     ]
    }
   ],
   "source": [
    "for (condition_name, num_sequenced_bps_per_group) in num_sequenced_bps_per_group_per_condition.items():\n",
    "    total_bps = sum(num_sequenced_bps_per_group.values())\n",
    "    throughput_reduction = sum(num_sequenced_bps_per_group_per_condition[\"control\"].values()) / sum(num_sequenced_bps_per_group.values())\n",
    "    \n",
    "    bps_per_target_str = \", \".join(f\"{group}: {num_bps:.2E}\" for (group, num_bps) in num_sequenced_bps_per_group.items())\n",
    "    print(f\"{condition_name:20}: total: {total_bps:.2E} ({throughput_reduction:.3}), {bps_per_target_str}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Absolute enrichment of target in condition enrich_chr_1_8      : 1.4\n",
      "Relative enrichment of target in condition enrich_chr_1_8      : 1.75\n",
      "Absolute enrichment of target in condition enrich_chr_9_14     : 2.04\n",
      "Relative enrichment of target in condition enrich_chr_9_14     : 2.82\n",
      "Absolute enrichment of target in condition enrich_chr_16_20    : 2.7\n",
      "Relative enrichment of target in condition enrich_chr_16_20    : 4.14\n"
     ]
    }
   ],
   "source": [
    "from simreaduntil.simulator.gap_sampling.gap_sampler_per_window_until_blocked import dict_without_items\n",
    "\n",
    "absolute_enrichment = {\n",
    "    condition_name: seq_bps_per_target[condition_name] / num_sequenced_bps_per_group_per_condition[\"control\"][condition_name]\n",
    "    for (condition_name, seq_bps_per_target) in dict_without_items(num_sequenced_bps_per_group_per_condition, [\"control\"]).items()\n",
    "}\n",
    "\n",
    "# relative composition when no selective sequencing is happening\n",
    "composition_noselseq = {\n",
    "    \"enrich_chr_1_8\": 0.496,\n",
    "    \"enrich_chr_9_14\": 0.247,\n",
    "    \"enrich_chr_16_20\": 0.125\n",
    "}\n",
    "relative_enrichment = {\n",
    "    condition_name: (seq_bps_per_target[condition_name] / sum(seq_bps_per_target.values())) / composition_noselseq[condition_name]\n",
    "    for (condition_name, seq_bps_per_target) in dict_without_items(num_sequenced_bps_per_group_per_condition, [\"control\"]).items()\n",
    "}\n",
    "\n",
    "for (condition_name, enrichment) in absolute_enrichment.items():\n",
    "    print(f\"Absolute enrichment of target in condition {condition_name:20}: {enrichment:.3}\")\n",
    "    print(f\"Relative enrichment of target in condition {condition_name:20}: {relative_enrichment[condition_name]:.3}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "# aligned, fake mapper, accel10 (results_readfishexp_realreads_fakemapper_accel10)\n",
    "control             : total: 2.72E+09 (1.0 ), enrich_chr_16_20: 3.36E+08, enrich_chr_1_8: 1.35E+09, enrich_chr_9_14: 6.74E+08, other: 3.59E+08\n",
    "enrich_chr_1_8      : total: 2.28E+09 (1.19), enrich_chr_16_20: 2.09E+07, enrich_chr_1_8: 2.20E+09, enrich_chr_9_14: 4.03E+07, other: 2.19E+07\n",
    "enrich_chr_9_14     : total: 1.99E+09 (1.36), enrich_chr_16_20: 3.27E+07, enrich_chr_1_8: 1.31E+08, enrich_chr_9_14: 1.79E+09, other: 3.49E+07\n",
    "enrich_chr_16_20    : total: 1.69E+09 (1.61), enrich_chr_16_20: 1.35E+09, enrich_chr_1_8: 1.92E+08, enrich_chr_9_14: 9.56E+07, other: 5.17E+07\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.63\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.94\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 2.66\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 3.65\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 4.0\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 6.39\n",
    "\n",
    "# aligned, realmapper, accel5 (results_readfishexp_realreads_realmapper_accel5)\n",
    "control             : total: 2.72E+09 (1.0 ), enrich_chr_16_20: 3.38E+08, enrich_chr_1_8: 1.35E+09, enrich_chr_9_14: 6.70E+08, other: 3.65E+08\n",
    "enrich_chr_1_8      : total: 2.31E+09 (1.18), enrich_chr_16_20: 3.01E+07, enrich_chr_1_8: 2.16E+09, enrich_chr_9_14: 6.96E+07, other: 4.90E+07\n",
    "enrich_chr_9_14     : total: 2.03E+09 (1.34), enrich_chr_16_20: 4.51E+07, enrich_chr_1_8: 1.71E+08, enrich_chr_9_14: 1.72E+09, other: 1.01E+08\n",
    "enrich_chr_16_20    : total: 1.73E+09 (1.58), enrich_chr_16_20: 1.28E+09, enrich_chr_1_8: 2.27E+08, enrich_chr_9_14: 1.31E+08, other: 9.46E+07\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.59\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.89\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 2.56\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 3.42\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 3.78\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 5.9\n",
    "\n",
    "# with unaligned, realmapper accel10 (results_readfishexp_realreads_realmapper_withunaligned_accel10)\n",
    "control             : total: 2.67E+09 (1.0), enrich_chr_16_20: 3.32E+08, enrich_chr_1_8: 1.33E+09, enrich_chr_9_14: 6.57E+08, other: 3.55E+08\n",
    "enrich_chr_1_8      : total: 2.32E+09 (1.15), enrich_chr_16_20: 2.26E+08, enrich_chr_1_8: 1.40E+09, enrich_chr_9_14: 4.52E+08, other: 2.44E+08\n",
    "enrich_chr_9_14     : total: 2.31E+09 (1.16), enrich_chr_16_20: 2.40E+08, enrich_chr_1_8: 9.53E+08, enrich_chr_9_14: 8.48E+08, other: 2.68E+08\n",
    "enrich_chr_16_20    : total: 2.27E+09 (1.18), enrich_chr_16_20: 4.90E+08, enrich_chr_1_8: 1.00E+09, enrich_chr_9_14: 5.00E+08, other: 2.74E+08\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.06\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.22\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 1.29\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 1.49\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 1.48\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 1.73\n",
    "\n",
    "# with unaligned, realmapper accel2 (results_readfishexp_realreads_realmapper_withunaligned_accel2)\n",
    "control             : total: 2.67E+09 (1.0), enrich_chr_16_20: 3.34E+08, enrich_chr_1_8: 1.32E+09, enrich_chr_9_14: 6.57E+08, other: 3.52E+08\n",
    "enrich_chr_1_8      : total: 2.15E+09 (1.24), enrich_chr_16_20: 6.55E+07, enrich_chr_1_8: 1.86E+09, enrich_chr_9_14: 1.37E+08, other: 8.44E+07\n",
    "enrich_chr_9_14     : total: 1.92E+09 (1.39), enrich_chr_16_20: 9.18E+07, enrich_chr_1_8: 3.61E+08, enrich_chr_9_14: 1.34E+09, other: 1.33E+08\n",
    "enrich_chr_16_20    : total: 1.74E+09 (1.54), enrich_chr_16_20: 8.91E+08, enrich_chr_1_8: 4.61E+08, enrich_chr_9_14: 2.40E+08, other: 1.44E+08\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.41\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.75\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 2.03\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 2.81\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 2.67\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 4.11\n",
    "\n",
    "# with unaligned, realmapper, accel3 (results_readfishexp_realreads_realmapper_withunaligned_accel3_longer)\n",
    "control             : total: 2.65E+09 (1.0), enrich_chr_16_20: 3.28E+08, enrich_chr_1_8: 1.32E+09, enrich_chr_9_14: 6.47E+08, other: 3.49E+08\n",
    "enrich_chr_1_8      : total: 2.13E+09 (1.24), enrich_chr_16_20: 6.44E+07, enrich_chr_1_8: 1.85E+09, enrich_chr_9_14: 1.33E+08, other: 8.19E+07\n",
    "enrich_chr_9_14     : total: 1.92E+09 (1.38), enrich_chr_16_20: 9.07E+07, enrich_chr_1_8: 3.55E+08, enrich_chr_9_14: 1.34E+09, other: 1.33E+08\n",
    "enrich_chr_16_20    : total: 1.73E+09 (1.53), enrich_chr_16_20: 8.92E+08, enrich_chr_1_8: 4.56E+08, enrich_chr_9_14: 2.39E+08, other: 1.42E+08\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.4\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.75\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 2.07\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 2.82\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 2.72\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 4.13\n",
    "\n",
    "# with unaligned, realmapper, accel5 (results_readfishexp_realreads_realmapper_withunaligned_accel5_longer)\n",
    "control             : total: 2.67E+09 (1.0), enrich_chr_16_20: 3.35E+08, enrich_chr_1_8: 1.32E+09, enrich_chr_9_14: 6.60E+08, other: 3.54E+08\n",
    "enrich_chr_1_8      : total: 2.12E+09 (1.26), enrich_chr_16_20: 6.32E+07, enrich_chr_1_8: 1.84E+09, enrich_chr_9_14: 1.33E+08, other: 8.11E+07\n",
    "enrich_chr_9_14     : total: 1.94E+09 (1.38), enrich_chr_16_20: 9.16E+07, enrich_chr_1_8: 3.60E+08, enrich_chr_9_14: 1.35E+09, other: 1.36E+08\n",
    "enrich_chr_16_20    : total: 1.75E+09 (1.53), enrich_chr_16_20: 9.05E+08, enrich_chr_1_8: 4.61E+08, enrich_chr_9_14: 2.40E+08, other: 1.43E+08\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.4\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.75\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 2.04\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 2.82\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 2.7\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 4.14\n",
    "\n",
    "\n",
    "## unused \n",
    "\n",
    "# short: with unaligned, realmapper accel5 (results_readfishexp_realreads_realmapper_withunaligned_accel5)\n",
    "control             : total: 1.82E+09 (1.0), enrich_chr_16_20: 2.23E+08, enrich_chr_1_8: 9.07E+08, enrich_chr_9_14: 4.47E+08, other: 2.39E+08\n",
    "enrich_chr_1_8      : total: 1.54E+09 (1.18), enrich_chr_16_20: 4.62E+07, enrich_chr_1_8: 1.34E+09, enrich_chr_9_14: 9.68E+07, other: 5.85E+07\n",
    "enrich_chr_9_14     : total: 1.36E+09 (1.33), enrich_chr_16_20: 6.51E+07, enrich_chr_1_8: 2.55E+08, enrich_chr_9_14: 9.48E+08, other: 9.54E+07\n",
    "enrich_chr_16_20    : total: 1.27E+09 (1.43), enrich_chr_16_20: 6.53E+08, enrich_chr_1_8: 3.34E+08, enrich_chr_9_14: 1.74E+08, other: 1.05E+08\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.47\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.75\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 2.12\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 2.82\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 2.93\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 4.13\n",
    "\n",
    "# for constant gap sampler (results_readfishexp_realreads_realmapper_withunaligned_constantgapsampler_accel5)\n",
    "control             : total: 2.27E+09 (1.0), enrich_chr_16_20: 2.82E+08, enrich_chr_1_8: 1.12E+09, enrich_chr_9_14: 5.63E+08, other: 3.00E+08\n",
    "enrich_chr_1_8      : total: 2.21E+09 (1.03), enrich_chr_16_20: 6.70E+07, enrich_chr_1_8: 1.92E+09, enrich_chr_9_14: 1.40E+08, other: 8.49E+07\n",
    "enrich_chr_9_14     : total: 2.15E+09 (1.05), enrich_chr_16_20: 1.03E+08, enrich_chr_1_8: 4.05E+08, enrich_chr_9_14: 1.49E+09, other: 1.51E+08\n",
    "enrich_chr_16_20    : total: 2.08E+09 (1.09), enrich_chr_16_20: 1.07E+09, enrich_chr_1_8: 5.56E+08, enrich_chr_9_14: 2.88E+08, other: 1.72E+08\n",
    "Absolute enrichment of target in condition enrich_chr_1_8      : 1.71\n",
    "Relative enrichment of target in condition enrich_chr_1_8      : 1.75\n",
    "Absolute enrichment of target in condition enrich_chr_9_14     : 2.65\n",
    "Relative enrichment of target in condition enrich_chr_9_14     : 2.81\n",
    "Absolute enrichment of target in condition enrich_chr_16_20    : 3.78\n",
    "Relative enrichment of target in condition enrich_chr_16_20    : 4.1\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1.41, 1.4929629629629628, 1.4478169014084508)"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# # yield-corrected\n",
    "# 1.49 * 1.23/1.24,\\\n",
    "# 2.2 * 1.44/1.89, \\\n",
    "# 3.04 * 1.7/2.84\n",
    "1.41 * 1.24/1.24,\\\n",
    "2.03 * 1.39/1.89, \\\n",
    "2.67 * 1.54/2.84"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# yield-corrected\n",
    "# 1.59 * 1.15/1.24, \\\n",
    "# 2.38 * 1.32/1.89, \\\n",
    "# 3.23 * 1.56/2.84"
   ]
  }
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