Merge pull request #3 from gitter-lab/tests-polishing

Add test case to check NetBox IL2 output

.travis.yml

@@ -12,3 +12,5 @@ script:
   - unzip -q referencePathways/reactome/reactomeGraphlets.zip -d referencePathways/reactome
   - cd scripts
   - bash runNetBoxIL2.sh
+  # Compare the generated IL2 output with the reference output
+  - cmp ../tests/reference/il2_ranking.txt il2_ranking.txt

README.md

@@ -1,8 +1,7 @@
-# pathway-parameter-advising
+# Pathway parameter advising
 [![Build Status](https://travis-ci.com/gitter-lab/pathway-parameter-advising.svg?branch=master)](https://travis-ci.com/gitter-lab/pathway-parameter-advising)
-Parameter advising for biological pathway creation algorithms
 
-Version 0.10. 
+Parameter advising for biological pathway creation algorithms.
 
 ## Dependencies
 
@@ -32,6 +31,13 @@ Arguments:
 >
 >  --verbose             If set, will print intermediate status updates. Optional, default = False.
 
+## Example
+
+`scripts/runNetBoxIL2.sh` runs pathway parameter advising for the precomputed graphlet files for NetBox IL2 pathways using Reactome reference pathways.
+It must be run from the `scripts` directory.
+Unzip the Reactome pathway graphlets file `reactomeGraphlets.zip` before running the example script.
+
 ## Graphlet Creation
 
-Graphlet decomposition files are created with  the [Parallel Graphlet Decomposition library](http://nesreenahmed.com/graphlets/). Files are the piped output from the pgd script: `./pgd inputGraphFile >> graphletOutputFile.gOut`.
+Graphlet decomposition files are created with  the [Parallel Graphlet Decomposition library](http://nesreenahmed.com/graphlets/).
+Files are the piped output from the pgd script: `./pgd inputGraphFile >> graphletOutputFile.gOut`.

scripts/pathwayParameterAdvising.py

@@ -1,9 +1,8 @@
 import os
 import argparse
-import networkx as nx
 import numpy as np
 import sys
-__version__ = 0.10
+__version__ = "0.1.0"
 
 """
 Author: Chris Magnano
@@ -16,7 +15,7 @@
 
 def main():
     #Handle command line arguments
-    parser = argparse.ArgumentParser(description="The pathway parameter advisor creates a ranking of pathways based on their topological distance to a set of reference pathways. Version %0.2f, released under the MIT liscense."%(__version__))
+    parser = argparse.ArgumentParser(description="The pathway parameter advisor creates a ranking of pathways based on their topological distance to a set of reference pathways. Version %s, released under the MIT license."%(__version__))
     parser.add_argument("--genPathwayGraphlets", help="File where each line is a graphlets file of a generated pathway.",required=True)
     parser.add_argument("--refPathwayGraphlets", help="File where each line is a graphlets file of a reference pathway.",required=True)
     parser.add_argument("--outFile", default="parameterRanking.txt", help="File to store output in.")

scripts/runNetBoxIL2.sh

@@ -1,3 +1,3 @@
 #Example using included IL2 data to run pathway parameter advising and get data
-python pathwayParameterAdvising.py --genPathwayGraphlets=../data/IL2/graphletNames.txt --refPathwayGraphlets=../referencePathways/reactomeGraphlets.txt --outFile=test --minSize=15 --outputScore --verbose
+python pathwayParameterAdvising.py --genPathwayGraphlets=../data/IL2/graphletNames.txt --refPathwayGraphlets=../referencePathways/reactomeGraphlets.txt --outFile=il2_ranking.txt --minSize=15 --outputScore --verbose
 

tests/reference/il2_ranking.txt

@@ -0,0 +1,127 @@
+Run	Score
+p8e-3	0.2125
+p9e-3	0.2132
+p1e-2	0.2133
+p7e-3	0.2135
+p6e-3	0.2140
+p5e-3	0.2147
+p2e-2	0.2149
+p4e-2	0.2162
+p3e-2	0.2163
+p5e-2	0.2164
+p6e-2	0.2171
+p7e-2	0.2174
+p8e-2	0.2174
+p9e-2	0.2174
+p3e-3	0.2199
+p4e-3	0.2201
+p2e-3	0.2277
+p1e-3	0.2741
+p9e-4	0.2802
+p8e-4	0.3008
+p7e-4	0.3115
+p6e-4	0.3219
+p5e-4	0.3434
+p2e-14	0.3518
+p3e-14	0.3518
+p4e-4	0.3854
+p3e-4	0.3954
+p2e-4	0.4059
+p1e-11	0.4124
+p1e-12	0.4124
+p1e-13	0.4124
+p2e-12	0.4124
+p2e-13	0.4124
+p3e-12	0.4124
+p3e-13	0.4124
+p4e-12	0.4124
+p4e-13	0.4124
+p4e-14	0.4124
+p5e-12	0.4124
+p5e-13	0.4124
+p5e-14	0.4124
+p6e-12	0.4124
+p6e-13	0.4124
+p6e-14	0.4124
+p7e-12	0.4124
+p7e-13	0.4124
+p7e-14	0.4124
+p8e-12	0.4124
+p8e-13	0.4124
+p8e-14	0.4124
+p9e-12	0.4124
+p9e-13	0.4124
+p9e-14	0.4124
+p1e-4	0.4516
+p9e-5	0.4573
+p8e-5	0.4672
+p7e-5	0.4852
+p6e-5	0.4964
+p1e-14	0.5187
+p1e-15	0.5187
+p2e-15	0.5187
+p3e-15	0.5187
+p4e-15	0.5187
+p5e-15	0.5187
+p6e-15	0.5187
+p7e-15	0.5187
+p8e-15	0.5187
+p9e-15	0.5187
+p5e-5	0.5415
+p4e-5	0.5485
+p3e-5	0.5496
+p2e-11	0.5697
+p3e-11	0.5697
+p2e-5	0.5733
+p1e-5	0.5898
+p9e-6	0.6027
+p4e-11	0.6069
+p5e-11	0.6069
+p6e-11	0.6069
+p7e-11	0.6069
+p8e-11	0.6069
+p9e-11	0.6069
+p8e-6	0.6207
+p7e-6	0.6333
+p5e-6	0.6509
+p6e-6	0.6509
+p3e-6	0.6581
+p4e-6	0.6581
+p2e-6	0.6754
+p1e-6	0.7404
+p1e-10	0.7533
+p2e-10	0.7533
+p3e-10	0.7663
+p4e-10	0.7663
+p5e-7	0.7677
+p6e-7	0.7733
+p7e-7	0.7733
+p8e-7	0.7733
+p9e-7	0.7765
+p1e-7	0.7848
+p2e-7	0.7848
+p3e-7	0.7848
+p4e-7	0.7848
+p5e-8	0.7848
+p6e-8	0.7848
+p7e-8	0.7848
+p8e-8	0.7848
+p9e-8	0.7848
+p4e-8	0.7899
+p3e-9	0.8013
+p4e-9	0.8013
+p5e-9	0.8013
+p2e-8	0.8091
+p3e-8	0.8091
+p1e-8	0.8147
+p6e-9	0.8147
+p7e-9	0.8147
+p8e-9	0.8147
+p9e-9	0.8147
+p5e-10	0.8246
+p6e-10	0.8246
+p7e-10	0.8246
+p1e-9	0.8252
+p8e-10	0.8252
+p9e-10	0.8252
+p2e-9	0.8301