{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "5a242f0d",
   "metadata": {},
   "source": [
    "# Library manipulation scripts\n",
    "\n",
    "This notebook showcases several useful commands that allow following library manipulations:\n",
    "\n",
    "- Library concatenation (`molli merge`)\n",
    "- Subset selection based on regular expression (`molli pick`)\n",
    "- Collect descriptive statistics (`molli stats`)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b257f789",
   "metadata": {},
   "source": [
    "## `molli merge`\n",
    "\n",
    "When several files (.mlib / .clib) are specified as positional arguments, those files are sequentially read (without interpretation!) and written into a new file.\n",
    "Linux style glob patterns are supported: `molli merge *.clib`\n",
    "\n",
    "**It is the user's responsibility to ensure homogeneous inputs**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2721d25c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "usage: molli merge [-h] -o <combined.mlib> [-c COMMENT] [--overwrite] [--sort]\n",
      "                   sources [sources ...]\n",
      "\n",
      "Merge several molli libraries into a single file\n",
      "\n",
      "positional arguments:\n",
      "  sources               List of library files (or glob patterns)\n",
      "\n",
      "options:\n",
      "  -h, --help            show this help message and exit\n",
      "  -o <combined.mlib>, --output <combined.mlib>\n",
      "                        Merge the files into this output file\n",
      "  -c COMMENT, --comment COMMENT\n",
      "                        Specify a text based comment to override the uKV\n",
      "                        default\n",
      "  --overwrite           Overwrite the target files if they exist (default is\n",
      "                        false)\n",
      "  --sort                Sort the keys before writing\n"
     ]
    }
   ],
   "source": [
    "!molli merge --help"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "af5babf3",
   "metadata": {},
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "2621ee72",
   "metadata": {},
   "source": [
    "## `molli pick`\n",
    "\n",
    "This script iterates over a library keys, attempting to match key to each of patterns specified as positional arguments that follow.\n",
    "For full documentation on regular expressions, see [Python re module documentation](https://docs.python.org/3/library/re.html)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "usage: molli pick [-h] [-f FILE] [-o <combined.mlib>] [--overwrite] [--sort]\n",
      "                  source [patterns ...]\n",
      "\n",
      "Merge several molli libraries into a single file\n",
      "\n",
      "positional arguments:\n",
      "  source                Library file\n",
      "  patterns              List of regular expressions to match\n",
      "\n",
      "options:\n",
      "  -h, --help            show this help message and exit\n",
      "  -f FILE, --file FILE  Specify the name patterns from file\n",
      "  -o <combined.mlib>, --output <combined.mlib>\n",
      "                        Merge the files into this output file\n",
      "  --overwrite           Overwrite the target files if they exist (default is\n",
      "                        false)\n",
      "  --sort                Sort the keys before writing\n"
     ]
    }
   ],
   "source": [
    "!molli pick --help"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "molli",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.11"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}