make rd_filter as a python package

MANIFEST.in

@@ -0,0 +1 @@
+graft rd_filters

README.md

@@ -1,4 +1,4 @@
-#### rd_filters.py
+# rd_filters
 
 This script provides a simple means of applying the 
 functional group filters from the ChEMBL database, as well as a number of 
@@ -21,43 +21,51 @@ documentation on the different alert sets.
 The SMARTS patterns in a number of these alerts were not compatible with the RDKit
 so I edited them.  A complete list of the changes I made is in the file **Notes.txt**. 
 
-#### Installation
+## Prerequisite
 
-This script has a few requirements
 * At least Python 3.6
-* The RDKit, you can find installation instructions [here](https://www.rdkit.org/docs/Install.html).  I'd recommend the conda route. 
-* The pandas and docopt libraries
-```python
-pip install pandas docopt
+* The RDKit, you can find installation instructions [here](https://www.rdkit.org/docs/Install.html).  I'd recommend the conda route.
+
+## Installation
+
+### Directly install from github
+
+`pip install git+https://github.com/PatWalters/rd_filters.git`
+
+### Local install
+
+``` shell
+git clone https://github.com/PatWalters/rd_filters
+cd rd_filters
+pip install .
 ```
-The script needs 3 files to operate. 
-* rd_filters.py - the main Python script. 
+
+## Usage
+
+The script needs 2 files to operate.
+
 * alert_collection.csv - the set of structural alerts
 * rules.json - the configuration file
 
-The script uses the following logic to find alert_collection.csv and 
-rules.json. 
-1.  Use locations specified by the "--alert" (for alerts.csv) and 
-"--rules" (for rules.json) command line arguments.
-2.  Look in the current directory.
-3.  Look in the directory pointed to by the FILTER_RULES_DATA environment variable.
+The script uses the following logic to find alert_collection.csv and rules.json.
 
+1. Use locations specified by the "--alert" (for alerts.csv) and "--rules" (for rules.json) command line arguments.
+2. Look in the current directory.
+3. Look in the directory pointed to by the FILTER_RULES_DATA environment variable.
 
 I'll provide some examples below to illustrate.  
 
-
 That's it, at this point you should be good to go. 
 
-#### Configuration files
+### Configuration files
 
 The file **alert_collection.csv** contains alerts.  You shouldn't have to mess with this unless you
-want to add your own structural alerts. I think the format is pretty obvious. 
+want to add your own structural alerts. I think the format is pretty obvious.
 
-The file **rules.json** controls which filters and alerts are used.  You can use the command 
+The file **rules.json** controls which filters and alerts are used.  You can use the command
 below to generate a **rules.json** with the default settings. 
-```
-rd_filters.py template --out rules.json
-```
+
+`rd_filters template --out rules.json`
 
 The **rules.json** file looks like this. The values for the properties are the maximum and minimum 
 allowed (inclusive).  To set which structural alerts are used, set **true** and **false**. You can 
@@ -95,28 +103,27 @@ Just edit the file with your [favorite text editor](https://www.gnu.org/software
         200
     ]
 }
-``` 
+```
 
 #### Examples
 
 First off, you're going to want to copy **alert_collection.csv** and 
 **rules.json** to a directory and set the FILTER_RULES_DATA environment
 variable to point to that directory.  If you are using a bash-ish shell
-and the files are in /home/elvis/data that would be: 
-```
-export FILTER_RULES_DATA=/home/elvis/data
+and the files are in /home/elvis/data that would be:
 
-```
+`export FILTER_RULES_DATA=/home/elvis/data`
 
 If you type
-```
-rd_filters.py -h 
-```
-you'll see this: 
-```
+
+`rd_filters -h`
+
+you'll see this:
+
+``` shell
 Usage:
-rd_filters.py filter --in INPUT_FILE --prefix PREFIX [--rules RULES_FILE_NAME] [--alerts ALERT_FILE_NAME][--np NUM_CORES]
-rd_filters.py template --out TEMPLATE_FILE [--rules RULES_FILE_NAME]
+rd_filters filter --in INPUT_FILE --prefix PREFIX [--rules RULES_FILE_NAME] [--alerts ALERT_FILE_NAME][--np NUM_CORES]
+rd_filters template --out TEMPLATE_FILE [--rules RULES_FILE_NAME]
 
 Options:
 --in INPUT_FILE input file name
@@ -131,9 +138,8 @@ Options:
 The basic operation is pretty simple. If I want to filter a file called test.smi and 
 I want my output files to start with "out", I could do something like this:
 
-```
-rd_filters.py filter --in test.smi --prefix out
-```
+`rd_filters filter --in test.smi --prefix out`
+
 This will create 2 files
 * **out.smi** - contains the SMILES strings and molecule names for all of the compounds
 passing the filters
@@ -142,28 +148,22 @@ by a molecule
 
 By default, this script runs in parallel and uses all available processors.  To
 change this value, use the --np flag. 
-```
-rd_filters.py filter --in test.smi --prefix out --np 4
-```
+
+`rd_filters filter --in test.smi --prefix out --np 4`
 
 As mentioned above, alternate rules files or alerts files can be specified on
 the command line.
-```
-rd_filters.py filter --in test.smi --prefix out --rules myrules.json
-rd_filters.py filter --in test.smi --prefix out --alerts myalerts.csv
-rd_filters.py filter --in test.smi --prefix out --rules myrules.json --alerts myalerts.csv
 
-```
-A new default rules template file can be generated using the **template** option. 
-```
-rdfilters.py template --out myrules.json
+``` shell
+rd_filters filter --in test.smi --prefix out --rules myrules.json
+rd_filters filter --in test.smi --prefix out --alerts myalerts.csv
+rd_filters filter --in test.smi --prefix out --rules myrules.json --alerts myalerts.csv
 ```
 
-As always please let me know if you have questions, comments, etc. 
-
-Pat Walters, August 2018
-
-
+A new default rules template file can be generated using the **template** option.
 
+`rdfilters.py template --out myrules.json`
 
+As always please let me know if you have questions, comments, etc. 
 
+Pat Walters, August 2018

rd_filters.py → rd_filters/rd_filters.py

@@ -10,10 +10,12 @@
 import os
 import json
 from docopt import docopt
+import pkg_resources
+
 
 cmd_str = """Usage:
-rd_filters.py filter --in INPUT_FILE --prefix PREFIX [--rules RULES_FILE_NAME] [--alerts ALERT_FILE_NAME][--np NUM_CORES]
-rd_filters.py template --out TEMPLATE_FILE [--rules RULES_FILE_NAME]
+rd_filters filter --in INPUT_FILE --prefix PREFIX [--rules RULES_FILE_NAME] [--alerts ALERT_FILE_NAME][--np NUM_CORES]
+rd_filters template --out TEMPLATE_FILE [--rules RULES_FILE_NAME]
 
 Options:
 --in INPUT_FILE input file name
@@ -77,7 +79,7 @@ def default_rule_template(alert_list, file_name):
 
 def get_config_file(file_name, environment_variable):
     """
-    Read a configuration file, first look for the file in the current directory, if you can't find
+    Read a configuration file, first look for the file, if you can't find
     it there, look in the directory pointed to by environment_variable
     :param file_name: the configuration file
     :param environment_variable: the environment variable
@@ -92,12 +94,12 @@ def get_config_file(file_name, environment_variable):
             if os.path.exists(config_file_path):
                 return config_file_path
 
-    error_list = [f"Could not file {file_name} in the current directory"]
+    error_list = [f"Could not file {file_name}"]
     if config_dir:
         err_str = f"Could not find {config_file_path} based on the {environment_variable}" + \
                   "environment variable"
         error_list.append(err_str)
-    error_list.append(f"Please put {file_name} in the current directory")
+    error_list.append(f"Please check {file_name} exists")
     error_list.append(f"Or in the directory pointed to by the {environment_variable} environment variable")
     print("\n".join(error_list))
     sys.exit(1)
@@ -152,7 +154,7 @@ def evaluate(self, lst_in):
 
 def main():
     cmd_input = docopt(cmd_str)
-    alert_file_name = cmd_input.get("--alerts") or "alert_collection.csv"
+    alert_file_name = cmd_input.get("--alerts") or pkg_resources.resource_filename('rd_filters', "data/alert_collection.csv")
     rf = RDFilters(alert_file_name)
 
     if cmd_input.get("template"):
@@ -161,7 +163,7 @@ def main():
 
     elif cmd_input.get("filter"):
         input_file_name = cmd_input.get("--in")
-        rules_file_name = cmd_input.get("--rules") or "rules.json"
+        rules_file_name = cmd_input.get("--rules") or pkg_resources.resource_filename('rd_filters', "data/rules.json")
         rules_file_path = get_config_file(rules_file_name, "FILTER_RULES_DATA")
         prefix_name = cmd_input.get("--prefix")
         num_cores = cmd_input.get("--np") or mp.cpu_count()

setup.py

@@ -0,0 +1,15 @@
+from setuptools import setup, find_packages
+
+
+setup(
+    name="rd_filters",
+    version="0.1",
+    packages=find_packages(),
+    entry_points={
+        'console_scripts': [
+            'rd_filters=rd_filters.rd_filters:main',
+        ],
+    },
+    install_requires=['pandas', 'docopt'],
+    include_package_data=True,
+)