diff --git a/docs/examples/cli/introduction_cli.ipynb b/docs/examples/cli/introduction_cli.ipynb index 9df6a01..37df136 100644 --- a/docs/examples/cli/introduction_cli.ipynb +++ b/docs/examples/cli/introduction_cli.ipynb @@ -2,33 +2,39 @@ "cells": [ { "cell_type": "markdown", - "source": [ - "# Introduction" - ], "metadata": { "collapsed": false, "pycharm": { "name": "#%% md\n" } - } + }, + "source": [ + "# Introduction" + ] }, { "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" } - } + }, + "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." + ] }, { "cell_type": "code", "execution_count": 1, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -55,29 +61,29 @@ "source": [ "%%bash\n", "openvar --help" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } - } + ] }, { "cell_type": "markdown", - "source": [ - "### ***Cat*** command" - ], "metadata": { "collapsed": false, "pycharm": { "name": "#%% md\n" } - } + }, + "source": [ + "### **Cat** command" + ] }, { "cell_type": "code", "execution_count": 2, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -99,29 +105,29 @@ "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" } - } + }, + "source": [ + "### **Count** command" + ] }, { "cell_type": "code", "execution_count": 3, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -145,29 +151,29 @@ "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" } - } + }, + "source": [ + "### **Group by** command" + ] }, { "cell_type": "code", "execution_count": 4, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -195,29 +201,29 @@ "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" } - } + }, + "source": [ + "### **Plugin** command" + ] }, { "cell_type": "code", "execution_count": 5, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -237,13 +243,7 @@ "source": [ "%%bash\n", "openvar plugin --help" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } - } + ] } ], "metadata": { @@ -267,4 +267,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +} diff --git a/docs/examples/cli/main_cli.ipynb b/docs/examples/cli/main_cli.ipynb index dd58f6b..2d476e6 100644 --- a/docs/examples/cli/main_cli.ipynb +++ b/docs/examples/cli/main_cli.ipynb @@ -37,7 +37,7 @@ } }, "source": [ - "### ***Cat*** command\n", + "### **Cat** command\n", "\n", "A simple case of the command:" ] @@ -118,7 +118,7 @@ } }, "source": [ - "### ***Count*** command\n", + "### **Count** command\n", "\n", "A simple case of the command:" ] @@ -231,7 +231,7 @@ } }, "source": [ - "### ***Group by*** command\n", + "### **Group by** command\n", "\n", "A simple case of the command:" ] @@ -354,7 +354,7 @@ }, "source": [ "\n", - "### ***Plugin*** command\n", + "### **Plugin** command\n", "\n", "_Plugin_ is slightly different than the others commands.\n", "\n", diff --git a/docs/examples/tasks/count.ipynb b/docs/examples/tasks/count.ipynb index 15957ef..cd9c55a 100644 --- a/docs/examples/tasks/count.ipynb +++ b/docs/examples/tasks/count.ipynb @@ -2,31 +2,37 @@ "cells": [ { "cell_type": "markdown", - "source": [ - "# _Count_" - ], "metadata": { "collapsed": false, "pycharm": { "name": "#%% md\n" } - } + }, + "source": [ + "# _Count_" + ] }, { "cell_type": "markdown", - "source": [ - "A simple example where we can find how **count** task works. This task is able with command-line." - ], "metadata": { "collapsed": false, "pycharm": { "name": "#%% md\n" } - } + }, + "source": [ + "A simple example where we can find how **count** task works. This task is able with command-line." + ] }, { "cell_type": "code", "execution_count": 1, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [], "source": [ "from os import getcwd\n", @@ -35,16 +41,16 @@ "\n", "dataset_folder = f'{dirname(getcwd())}/datasets/sample2'\n", "annotation_path = f'{dirname(getcwd())}/datasets/sample2/annotation.yaml'" - ], + ] + }, + { + "cell_type": "markdown", "metadata": { "collapsed": false, "pycharm": { - "name": "#%%\n" + "name": "#%% md\n" } - } - }, - { - "cell_type": "markdown", + }, "source": [ "`count` task allows us to count the number of rows that result has. It has the following parameters:\n", "\n", @@ -56,17 +62,17 @@ "- `quite` - Do not show the progress meanwhile the parsing is running.\n", "\n", "On the following example we can see a general case of `count` task:" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } - } + ] }, { "cell_type": "code", "execution_count": 2, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -79,16 +85,16 @@ "source": [ "result = count(base_path=dataset_folder, annotation_path=annotation_path, quite=True)\n", "print(f\"Total: {result[0]}\")" - ], + ] + }, + { + "cell_type": "markdown", "metadata": { "collapsed": false, "pycharm": { - "name": "#%%\n" + "name": "#%% md\n" } - } - }, - { - "cell_type": "markdown", + }, "source": [ "One of the parameter on `count` task is `where`. You will be able to apply a conditional filter. The possible operations can be:\n", "\n", @@ -99,18 +105,18 @@ "+ `>=` - More or equal than.\n", "+ `>` - More than.\n", "\n", - "Also, `gropu_by` to group rows on different values of this key. An example of these parameters is the following one:" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } - } + "Also, `group_by` to group rows on different values of this key. An example of these parameters is the following one:" + ] }, { "cell_type": "code", "execution_count": 3, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -125,13 +131,7 @@ "result = count(base_path=dataset_folder, annotation_path=annotation_path, where=\"SYMBOL == 'ATAD3C'\", group_by=\"CANCER\", quite=True)\n", "print(f\"Total: {result[0]}\")\n", "print(f\"Groups and count: {result[1]}\")" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } - } + ] } ], "metadata": { @@ -155,4 +155,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +} diff --git a/docs/release_notes.rst b/docs/release_notes.rst index 311d6a4..5da280c 100644 --- a/docs/release_notes.rst +++ b/docs/release_notes.rst @@ -1,11 +1,21 @@ +============= +Release Notes +============= -********************* -Release notes -********************* +Version history +-------------------- -Version 0.1 -=============================== ++------------+----------+----------------------------------------+----------------------+ +| **Date** | **Ver.** | **Author** | **Comment** | ++------------+----------+----------------------------------------+----------------------+ +| 2024-07-25 | 1.0.0 | `@bbglab `_ | First stable release | +| | | | | ++------------+----------+----------------------------------------+----------------------+ -Version 0.X -=============================== -gfrfrfr \ No newline at end of file +OpenVariant v1.0.0 +================== + +First stable release of OpenVariant. This version includes the following features: + +* Tasks: **find** files, **cat** operation and **group-by**. +* Plugin system: classification of **alteration type**, **alternate allele frequency** getter and **LiftOver** operation. \ No newline at end of file diff --git a/examples/tasks/count.ipynb b/examples/tasks/count.ipynb index 15957ef..cd9c55a 100644 --- a/examples/tasks/count.ipynb +++ b/examples/tasks/count.ipynb @@ -2,31 +2,37 @@ "cells": [ { "cell_type": "markdown", - "source": [ - "# _Count_" - ], "metadata": { "collapsed": false, "pycharm": { "name": "#%% md\n" } - } + }, + "source": [ + "# _Count_" + ] }, { "cell_type": "markdown", - "source": [ - "A simple example where we can find how **count** task works. This task is able with command-line." - ], "metadata": { "collapsed": false, "pycharm": { "name": "#%% md\n" } - } + }, + "source": [ + "A simple example where we can find how **count** task works. This task is able with command-line." + ] }, { "cell_type": "code", "execution_count": 1, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [], "source": [ "from os import getcwd\n", @@ -35,16 +41,16 @@ "\n", "dataset_folder = f'{dirname(getcwd())}/datasets/sample2'\n", "annotation_path = f'{dirname(getcwd())}/datasets/sample2/annotation.yaml'" - ], + ] + }, + { + "cell_type": "markdown", "metadata": { "collapsed": false, "pycharm": { - "name": "#%%\n" + "name": "#%% md\n" } - } - }, - { - "cell_type": "markdown", + }, "source": [ "`count` task allows us to count the number of rows that result has. It has the following parameters:\n", "\n", @@ -56,17 +62,17 @@ "- `quite` - Do not show the progress meanwhile the parsing is running.\n", "\n", "On the following example we can see a general case of `count` task:" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } - } + ] }, { "cell_type": "code", "execution_count": 2, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -79,16 +85,16 @@ "source": [ "result = count(base_path=dataset_folder, annotation_path=annotation_path, quite=True)\n", "print(f\"Total: {result[0]}\")" - ], + ] + }, + { + "cell_type": "markdown", "metadata": { "collapsed": false, "pycharm": { - "name": "#%%\n" + "name": "#%% md\n" } - } - }, - { - "cell_type": "markdown", + }, "source": [ "One of the parameter on `count` task is `where`. You will be able to apply a conditional filter. The possible operations can be:\n", "\n", @@ -99,18 +105,18 @@ "+ `>=` - More or equal than.\n", "+ `>` - More than.\n", "\n", - "Also, `gropu_by` to group rows on different values of this key. An example of these parameters is the following one:" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } - } + "Also, `group_by` to group rows on different values of this key. An example of these parameters is the following one:" + ] }, { "cell_type": "code", "execution_count": 3, + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [ { "name": "stdout", @@ -125,13 +131,7 @@ "result = count(base_path=dataset_folder, annotation_path=annotation_path, where=\"SYMBOL == 'ATAD3C'\", group_by=\"CANCER\", quite=True)\n", "print(f\"Total: {result[0]}\")\n", "print(f\"Groups and count: {result[1]}\")" - ], - "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } - } + ] } ], "metadata": { @@ -155,4 +155,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +}