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Merge pull request #46 from bbglab/18-openvariant-dont-fail-if-folderfile-permission-denied
18 OpenVariant Dont fail if folderfile permission denied
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‎docs/examples/cli/introduction_cli.ipynb

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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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}
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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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}
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"execution_count": 1,
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"metadata": {
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"collapsed": false,
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%%\n"
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}
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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 1,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%%\n"
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}
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" -a, --annotations PATH Annotation path. eg: /path/annotation_vcf.yaml\n",
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" --header Show the result header.\n",
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" -o, --output TEXT File to write the output.\n",
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" --skip Skip files and directories that are unreadable.\n",
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" -h, --help Show this message and exit.\n"
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]
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}
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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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}
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 2,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%%\n"
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}
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" -c, --cores INTEGER Maximum processes to run in parallel.\n",
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" -q, --quite Don't show the progress.\n",
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" -o, --output TEXT File to write the output.\n",
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" --skip Skip files and directories that are unreadable.\n",
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" -h, --help Show this message and exit.\n"
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]
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}
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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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},
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"pycharm": {
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"name": "#%%\n"
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}
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" -c, --cores INTEGER Maximum processes to run in parallel.\n",
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" -q, --quite Don't show the progress.\n",
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" -o, --output TEXT File to write the output.\n",
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" --skip Skip files and directories that are unreadable.\n",
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" -h, --help Show this message and exit.\n"
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]
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}
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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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}
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%%\n"
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" Actions to apply on the plugin system.\n",
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"\n",
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"Options:\n",
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" -n, --name TEXT Name of the plugin.\n",
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" -d, --directory TEXT Directory to reach the plugin.\n",
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" -h, --help Show this message and exit.\n"
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" -n, --name TEXT Name of the plugin.\n",
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" -h, --help Show this message and exit.\n"
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]
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}
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],
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.6"
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"pygments_lexer": "ipython3",
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"version": "3.13.2"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎docs/examples/find_files/find_files_with_directory_path.ipynb

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},
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{
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"cell_type": "markdown",
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"source": [
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"A Simple example on how find files task works for a directory path."
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],
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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}
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}
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},
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"source": [
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"A Simple example on how find files task works for a directory path."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%%\n"
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}
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},
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"outputs": [],
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"source": [
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"from os import getcwd\n",
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"from os.path import dirname\n",
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"from openvariant import findfiles\n",
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"\n",
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"dataset_folder = f'{dirname(getcwd())}/datasets/sample1'"
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],
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]
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},
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{
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"cell_type": "markdown",
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%% md\n"
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},
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"source": [
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"It will get any type of file that matches with any _annotation_ file that is on the same folder or in a child folder.\n",
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"\n",
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"`find_files` function parameters:\n",
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"\n",
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"- `base_path` - Base path of _input_ folder.\n",
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"- `annotation_path` - Path of _annotation_ file.\n",
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"- `skip_files` - Skip unreadable files and directories.\n",
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"\n",
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"As we see, the output has two types of pattern `*.vcf.gz` and `*.maf.gz`.\n"
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"name": "#%% md\n"
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]
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"jupyter": {
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"outputs_hidden": false
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},
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"pycharm": {
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"name": "#%%\n"
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},
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" print(f'File path: {file_path}')\n",
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" print(f'Annotation object: {annotation}')\n",
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" print(\"-------------------------------------\")"
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"name": "#%%\n"
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]
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{
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"cell_type": "markdown",
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"source": [
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"In the following example, we will get files with a fixed _Annotation_ file.\n",
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"\n",
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"All the files that we will be able to detect will follow the pattern described on annotations."
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],
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"metadata": {
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"jupyter": {
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},
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"name": "#%% md\n"
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}
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},
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"source": [
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"In the following example, we will get files with a fixed _Annotation_ file.\n",
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"\n",
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"All the files that we will be able to detect will follow the pattern described on annotations."
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]
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},
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"name": "#%%\n"
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]
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"pygments_lexer": "ipython3",
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"version": "3.8.12"
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"version": "3.10.16"
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"nbformat": 4,
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}
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"nbformat_minor": 4
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}

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