fix: added requirements for docs

bbglab · Jul 29, 2022 · b9d3edc · b9d3edc
1 parent 7af724c
commit b9d3edc
Show file tree

Hide file tree

Showing 21 changed files with 2,363 additions and 5 deletions.
diff --git a/.gitignore b/.gitignore
@@ -115,9 +115,4 @@ out/
 atlassian-ide-plugin.xml
 
 # Documentation
-docs/examples/find_files
-docs/examples/variant
-docs/examples/tasks
-docs/examples/cli
-docs/examples/plugin_system
 docs/_build/
diff --git a/docs/examples/cli/README.md b/docs/examples/cli/README.md
@@ -0,0 +1,4 @@
+# Command-line examples
+
+- [Introduction](introduction_cli.ipynb) - Description of each command that offers *OpenVariant* with `openvar`.
+- [Main](main_cli.ipynb) - Bunch of examples that can be run in a shell.
diff --git a/docs/examples/cli/introduction_cli.ipynb b/docs/examples/cli/introduction_cli.ipynb
@@ -0,0 +1,270 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Introduction"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "**OpenVariant** offers a command-line interface (CLI) with the main tasks that also can be applied in Python scripts.\n",
+    "\n",
+    "On the following command you can check the different options that `openvar` can run."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Usage: openvar [OPTIONS] COMMAND [ARGS]...\n",
+      "\n",
+      "  'openvar' is the command-line interface of OpenVariant. Parsing and data\n",
+      "  transformation of multiple input formats.\n",
+      "\n",
+      "Options:\n",
+      "  --version   Show the version and exit.\n",
+      "  -h, --help  Show this message and exit.\n",
+      "\n",
+      "Commands:\n",
+      "  cat      Concatenate parsed files to standard output.\n",
+      "  count    Number of rows that matches a specified criterion.\n",
+      "  groupby  Group the parsed result for each different value of the specified\n",
+      "           key.\n",
+      "  plugin   Actions to execute for a plugin: create.\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%bash\n",
+    "openvar --help"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### ***Cat*** command"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Usage: openvar cat [OPTIONS] [INPUT_PATH]\n",
+      "\n",
+      "  Print the parsed files on the stdout/\"output\".\n",
+      "\n",
+      "Options:\n",
+      "  -w, --where TEXT        Filter expression. eg: CHROMOSOME == 4\n",
+      "  -a, --annotations PATH  Annotation path. eg: /path/annotation_vcf.yaml\n",
+      "  --header                Show the result header.\n",
+      "  -o, --output TEXT       File to write the output.\n",
+      "  -h, --help              Show this message and exit.\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%bash\n",
+    "openvar cat --help"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### ***Count*** command"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Usage: openvar count [OPTIONS] [INPUT_PATH]\n",
+      "\n",
+      "  Print on the stdout/\"output\" the number of rows that meets the criteria.\n",
+      "\n",
+      "Options:\n",
+      "  -w, --where TEXT        Filter expression. eg: CHROMOSOME == 4\n",
+      "  -g, --group_by TEXT     Key to group rows. eg: COUNTRY\n",
+      "  -a, --annotations PATH  Annotation path. eg: /path/annotation_vcf.yaml\n",
+      "  -c, --cores INTEGER     Maximum processes to run in parallel.\n",
+      "  -q, --quite             Don't show the progress.\n",
+      "  -o, --output TEXT       File to write the output.\n",
+      "  -h, --help              Show this message and exit.\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%bash\n",
+    "openvar count --help"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### ***Group by*** command"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Usage: openvar groupby [OPTIONS] [INPUT_PATH]\n",
+      "\n",
+      "  Print on the stdout/\"output\" the parsed files group by a specified field.\n",
+      "\n",
+      "Options:\n",
+      "  --header                Show the result header.\n",
+      "  --show                  Show group by each row.\n",
+      "  -w, --where TEXT        Filter expression. eg: CHROMOSOME == 4\n",
+      "  -g, --group_by TEXT     Key to group rows. eg: COUNTRY\n",
+      "  -s, --script TEXT       Filter expression. eg: gzip >\n",
+      "                          \\${GROUP_KEY}.parsed.tsv.gz\n",
+      "  -a, --annotations PATH  Annotation path. eg: /path/annotation_vcf.yaml\n",
+      "  -c, --cores INTEGER     Maximum processes to run in parallel.\n",
+      "  -q, --quite             Don't show the progress.\n",
+      "  -o, --output TEXT       File to write the output.\n",
+      "  -h, --help              Show this message and exit.\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%bash\n",
+    "openvar groupby --help"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### ***Plugin*** command"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Usage: openvar plugin [OPTIONS] {create}\n",
+      "\n",
+      "  Actions to apply on the plugin system.\n",
+      "\n",
+      "Options:\n",
+      "  -n, --name TEXT       Name of the plugin.\n",
+      "  -d, --directory TEXT  Directory to reach the plugin.\n",
+      "  -h, --help            Show this message and exit.\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%bash\n",
+    "openvar plugin --help"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}