# mirna-pathway-finder
Find pathways with [microRNAs](http://www.ncbi.nlm.nih.gov/pubmed/14744438) (miRNAs) at WikiPathways.

miRNAs can regulate gene expression through interactions with messenger RNAs (mRNAs). Although the actual interaction may be technically between the miRNA and mRNA, this process is often described more loosely as the miRNA *targeting* any one of the *gene*, the transcribed *mRNA* or the translated *protein*, as desired in the relevant context.

As a component for the Genboree workbench, this library:

1. takes as *input* a user-specified list of miRNAs
2. combines that input with pre-processed miRNA-to-gene mapping data, as described [here](https://github.com/nrnb/mirna-pathway-finder/blob/master/wp-mir-table-builder/wp-mir-table-hs-readme.txt)
3. produces as *output* a list of pathways that contain
  1. one or more miRNAs from the user-specified list, and/or 
  2. one or more genes that are targeted by one or more of the miRNAs from the user-specified list

The list is displayed as a table that looks like this:

| Pathway Title | Linkout | miRNAs on Pathway | Targets on Pathway (Targeting miRNAs) |
| --------------- | --------- | -------- | --------------- |
| Sample Pathway | [WP4](http://www.wikipathways.org/wpi/WP4) | 0 | 3 (1) |
| Sample Pathway | [WP5](http://www.wikipathways.org/wpi/WP4) | 2 | 3 (2) |
| Sample Pathway | [WP6](http://www.wikipathways.org/wpi/WP4) | 2 | 3 (1) |

## To install

```
git clone git@github.com:nrnb/mirna-pathway-finder.git
cd mirna-pathway-finder
```

Set up your virtualenv:

(how to install [virtualenv on Mac](http://exponential.io/blog/2015/02/10/install-virtualenv-and-virtualenvwrapper-on-mac-os-x/)) 

```
mkvirtualenv mirna-pathway-finder
```

or if you've already created this virtualenv:

```
workon mirna-pathway-finder
```

Install dependencies:

```
pip install -e .
```

## To run

Check command line argument defaults:

```
python mirnapathwayfinder/__init__.py -h
```

if the defaults are OK, you can then find pathways with miRNAs for a specific node_id:

```
python mirnapathwayfinder/__init__.py hsa-miR-370-3p
```

or provide a file path to a list of node_ids:

```
python mirnapathwayfinder/__init__.py 'tests/test1/input/node-list.txt'
```

Or you can override the defaults, e.g., override default output directory path:

```
python mirnapathwayfinder/__init__.py 'tests/test1/input/node-list.txt' -o 'tests/test1/output-actual/'
```

## Todo
* [x] Get command line arguments working
* [ ] Test
* [ ] Publish