getting click to work

README.md

@@ -4,6 +4,27 @@ Tool to detect potential transposable elements in a fasta file. Some classes of
 To solve this issue these TEs should be detected and removed in all genomes prior to doing a comparative analysis (e.g. counting genes, constructing gene families, ...). De-TE-ctor is a small pipeline to quickly check for putative TEs included in the set of protein coding genes of a genome and report them so they can be removed.
 
 
+## Usage
+
+### Installation
+
+Clone the package from the git repository
+
+    git clone https://github.molgen.mpg.de/proost/De-TE-ctor detector
+    cd detector
+
+Create a virtual environment
+
+    virtualenv --python=python3 venv
+    source env/bin/activate
+    pip install -r requirements.txt
+
+Install the detector module
+
+    pip install --editable .
+
+### Commands
+
 TODO
 
   * Collect sequences for known protein coding transposable elements.

detector.py

@@ -0,0 +1,30 @@
+import click
+
+
+@click.group()
+def cli():
+    """
+    Detector can be used to detect transposable elements in a fasta file.
+
+    usage: detector <command>
+
+    potential commands:
+        build : build the database
+        blast : blasts a fasta file agains a database
+        analyze : checks the blast output if TEs are present
+    """
+    pass
+
+
+@cli.command()
+@click.argument('path', type=click.path())
+def build(path):
+    """
+    Builds the blast database.
+
+    usage: detector build PATH (the directory with .fasta files to build the database)
+
+    """
+    click.echo("Building the database ... ")
+    click.echo("Input path: %s" % path)
+

requirements.txt

@@ -0,0 +1 @@
+click==6.7

setup.py

@@ -0,0 +1,14 @@
+from setuptools import setup
+
+setup(
+    name='DeTEctor',
+    version='0.1',
+    py_modules=['detector'],
+    install_requires=[
+        'Click',
+    ],
+    entry_points='''
+        [console_scripts]
+        detector=detector:cli
+    '''
+)