feat: new run and download command

The application now supports two main functions:
- `run` for generating the report
- `download` for downloading all supported databases

MANIFEST.in

@@ -1,4 +1,4 @@
 include LICENSE
 include README.md
-include docs/_src/_static/fusion-report.png
+include requirements.txt
 recursive-include fusion_report *

README.md

@@ -18,14 +18,23 @@ This python script generates an interactive summary report from fusion detection
 
 ## Installation
 
+### From source
+
 ```bash
+sudo apt-get install sqlite3 wget
 python3 setup.py install
 ```
 
 ## Usage
 
 ```bash
-fusion_report "<SAMPLE NAME>" /path/to/output /path/to/db/ 
+# Download required databases
+# Currently supported databases: FusionGDB, Mitelman and COSMIC
+# COSMIC requires login credentials to download Fusion gene Database
+fusion_report download --cosmic_usr '<username>' --cosmic_passwd '<password>' /path/to/db/
+
+# Run the fusion-report
+fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ 
   --ericscript tests/test_data/ericscript.tsv 
   --starfusion tests/test_data/starfusion.tsv 
   --fusioncatcher tests/test_data/fusioncatcher.txt
@@ -37,6 +46,8 @@ Or get help and list all possible parameters.
 
 ```bash
 fusion_report --help
+fusion_report run --help
+fusion_report download --help
 ```
 
 For more info on how to run the script, please see the [documentation](https://matq007.github.io/fusion-report/).

bin/fusion_report

@@ -8,6 +8,7 @@ from fusion_report.lib.report import Report
 from fusion_report.lib.section import Section
 from fusion_report.lib.graph import Graph
 from fusion_report.lib.tool_parser import ToolParser
+from fusion_report.lib.download import Download
 from fusion_report.core import tool_detection_chart, known_vs_unknown_chart, \
     distribution_chart, create_fusions_table, create_ppi_graph, print_progress_bar, \
     get_db_fusions, score_fusion, create_multiqc_section, create_fusion_list
@@ -30,6 +31,11 @@ def parse(params):
 
     return tools
 
+def download(params):
+    """ Function for downloading all databases. """
+    manager = Download(params)
+    manager.get_all_databases()
+
 def generate_index(params, parser):
     """
     Helper function for generating index.html page.
@@ -274,92 +280,135 @@ def main():
             Supported tools are: {0} and {1}.
         '''.format(', '.join(SUPPORTED_TOOLS[:-1]), SUPPORTED_TOOLS[-1])
     )
-    mandatory = parser.add_argument_group('Mandatory arguments', 'Required arguments to run app.')
-    mandatory.add_argument(
+    # fusion_parser run
+    subparsers = parser.add_subparsers(dest='command')
+    run_parser = subparsers.add_parser('run', help='Run application')
+    run_mandatory = run_parser.add_argument_group(
+        'Mandatory arguments', 'Required arguments to run app.'
+    )
+    run_mandatory.add_argument(
         'sample',
         help='Sample name',
         type=str
     )
-    mandatory.add_argument(
+    run_mandatory.add_argument(
         'output',
         help='Output directory',
         type=str
     )
-    mandatory.add_argument(
+    run_mandatory.add_argument(
         'db_path',
         help='Path to folder where all databases are stored.',
         type=str
     )
-    tools = parser.add_argument_group('Tools', 'List of all supported tools with their weights.')
-    tools.add_argument(
+    run_tools = run_parser.add_argument_group(
+        'Tools', 'List of all supported tools with their weights.'
+    )
+    run_tools.add_argument(
         '--ericscript',
         help='EricScript output file',
         type=str
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--ericscript_weight',
         help='EricScript weight',
         type=float,
         default=DEFAULT_TOOL_WEIGHT
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--fusioncatcher',
         help='FusionCatcher output file',
         type=str
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--fusioncatcher_weight',
         help='FusionCatcher weight',
         type=float,
         default=DEFAULT_TOOL_WEIGHT
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--starfusion',
         help='STAR-Fusion output file',
         type=str
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--starfusion_weight',
         help='STAR-Fusion weight',
         type=float,
         default=DEFAULT_TOOL_WEIGHT
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--pizzly',
         help='Pizzly output file',
         type=str
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--pizzly_weight',
         help='Pizzly weight',
         type=float,
         default=DEFAULT_TOOL_WEIGHT
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--squid',
         help='Squid output file',
         type=str
     )
-    tools.add_argument(
+    run_tools.add_argument(
         '--squid_weight',
         help='Squid weight',
         type=float,
         default=DEFAULT_TOOL_WEIGHT
     )
-    optional = parser.add_argument_group('Optional', 'List of additional configuration parameters.')
-    optional.add_argument(
+    run_optional = run_parser.add_argument_group(
+        'Optional', 'List of additional configuration parameters.'
+    )
+    run_optional.add_argument(
         '-c', '--config',
         help='Input config file',
         type=str,
         required=False
     )
-    optional.add_argument(
+    run_optional.add_argument(
         '-t', '--tool_cutoff',
         help='Number of tools required to detect a fusion',
         type=int,
         default=TOOL_DETECTION_CUTOFF
     )
-    generate_report(parser.parse_args())
+    # fusion_parser download
+    download_parser = subparsers.add_parser('download', help='Download required databases')
+    download_parser.add_argument(
+        'output',
+        help='Output directory',
+        type=str
+    )
+    mandatory_download = download_parser.add_argument_group(
+        'COSMIC', '''Option credential parameters. You can either provide username and password
+        which will be used to generate base64 token or the token itself.'''
+    )
+    mandatory_download.add_argument(
+        '--cosmic_usr',
+        help='COSMIC username',
+        type=str
+    )
+    mandatory_download.add_argument(
+        '--cosmic_passwd',
+        help='COSMIC password',
+        type=str
+    )
+    mandatory_download.add_argument(
+        '--cosmic_token',
+        help='COSMIC token',
+        type=str
+    )
+
+    # Handle individual commands
+    params = parser.parse_args()
+    if params.command == 'run':
+        generate_report(params)
+    elif params.command == 'download':
+        download(params)
+    else:
+        exit(f'Command {params.command} not recognized!')
 
 if __name__ == "__main__":
     main()

docs/_src/download_db.rst

@@ -7,6 +7,18 @@ Currently the tool supports three different databases:
 - Mitelman
 - COSMIC
 
+You can download the databases running:
+
+.. code-block:: bash
+
+    fusion_report download 
+        --cosmic_usr '<username>'
+        --cosmic_passwd '<password>'
+        /path/to/db
+
+Manual download
+***************
+
 FusionGDB
 ---------
 

docs/_src/lib.rst

@@ -4,6 +4,7 @@ Lib
 .. toctree::
 
    lib/db
+   lib/download
    lib/fusion_detail
    lib/graph
    lib/master_page

docs/_src/lib/download.rst

@@ -0,0 +1,5 @@
+Download
+===================
+
+.. autoclass:: fusion_report.lib.download.Download
+    :members:

docs/_src/usage.rst

@@ -8,7 +8,7 @@ Run all fusion detection tools
 
 .. code-block:: bash
 
-    fusion_report "<SAMPLE NAME>" /path/to/output /path/to/db/ 
+    fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ 
         --ericscript tests/test_data/ericscript.tsv 
         --starfusion tests/test_data/starfusion.tsv 
         --fusioncatcher tests/test_data/fusioncatcher.txt
@@ -23,7 +23,7 @@ equal `100 / (number of tools)`.
 
 .. code-block:: bash
 
-    fusion_report "<SAMPLE NAME>" /path/to/output /path/to/db/ 
+    fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ 
         --ericscript tests/test_data/ericscript.tsv 
         --ericscript_weight 30.5
         --fusioncatcher tests/test_data/fusioncatcher.txt
@@ -34,4 +34,6 @@ All parameters and options
 
 .. code-block:: bash
 
-    fusion_report --help
+    fusion_report --help
+    fusion_report run --help
+    fusion_report download --help