Merge pull request #5 from gitter-lab/integratedScript

Integrated script

.travis.yml

@@ -7,10 +7,11 @@ python:
 cache:
   - pip
 install:
-  - pip install networkx numpy 
+  - pip install networkx numpy
 script:
-  - unzip -q referencePathways/reactome/reactomeGraphlets.zip -d referencePathways/reactome
   - cd scripts
+  # Installs pgd, uses graph conversion script, and runs PPA
+  - bash runPPA.sh ../data/Wnt wnt_ranking.txt
   - bash runNetBoxIL2.sh
   # Compare the generated IL2 output with the reference output
   - cmp ../tests/reference/il2_ranking.txt il2_ranking.txt

README.md

@@ -5,7 +5,9 @@ Parameter advising for biological pathway creation algorithms.
 
 ## Dependencies
 
-Pathway parameter advising was written and tested using Python 3.6 and requires the packages `networkx` and `numpy`. 
+Pathway parameter advising was written and tested using Python 3.6 and requires the packages `networkx` and `numpy`.
+The `runPPA.sh` and `setupPGD.sh` scripts require git.
+These scripts have only been tested in a Linux environment initially.
 
 ## Usage
 
@@ -33,11 +35,23 @@ Arguments:
 
 ## Example
 
+`scripts/runPPA.sh` runs pathway parameter advising on any set of sif or edgelist networks.
+It will attempt to install the pgd library and setup the reactome pathway graphlets automatically. 
+The following commands will run `runPPA.sh` with the included `Wnt` and `Prolactin` datasets from the `scripts` directory:
+
+> `bash runPPA.sh ../data/Wnt wnt_ranking.txt`
+>
+> `bash runPPA.sh ../data/Prolactin prolactin_ranking.txt`
+
 `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 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`.
+Files are the piped output from the pgd script: `./pgd -f inputGraphFile >> graphletOutputFile.gOut`.
+
+`scripts/setupPGD.sh` installs the PGD library into the `lib` directory, which is created if none exists.
+PGD is cloned from its [github repository](https://github.com/nkahmed/pgd) and complied using `make`.
+It can then be run from the base pathway-parameter-advising directory as `lib/pgd/pgd -f inputGraphFile`.

data/IL2/README.md

@@ -1,7 +1,7 @@
 # IL2
 
-This directory holds pathway and graphlet files from reconstructing the [NetPath IL2 pathway](netpath.org/pathways?path_id=NetPath_14 "NetPath IL2 Pathway") from a 30% sample.
+This directory holds pathway and graphlet files from reconstructing the [NetPath IL2 pathway](http://netpath.org/pathways?path_id=NetPath_14 "NetPath IL2 Pathway") from a 30% sample.
 
 Pathways were generated using [NetBox](http://sanderlab.org/tools/netbox.html "NetBox Homepage") over a parameter sweep of the `p` parameter and are provided in .sif format. 
 
-Graphlet files are the output from the [Parallel Graphlet Decomposition library](http://nesreenahmed.com/graphlets/). Files are the piped output from the pgd script. 
+Graphlet files are the output from the [Parallel Graphlet Decomposition library](http://nesreenahmed.com/graphlets/). Files are the piped output from the pgd script. 

data/IL2/pathways/p1e-10.sif

@@ -1,159 +1,159 @@
-1	2
-1	3
-1	6
-1	8
-1	9
-1	10
-1	13
-1	14
-1	16
-1	24
-1	25
-1	26
-1	27
-1	28
-2	3
-2	5
-2	6
-2	8
-2	9
-2	10
-2	11
-2	12
-2	13
-2	14
-2	16
-2	20
-2	21
-2	24
-2	25
-2	26
-2	27
-2	28
-3	6
-3	8
-3	9
-3	10
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-4	9
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-4	25
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-5	7
-5	8
-5	9
-5	13
-5	16
-5	20
-5	21
-5	25
-5	26
-5	27
-5	28
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-6	9
-6	12
-6	14
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-6	24
-6	25
-6	27
-7	10
-7	19
-7	20
-8	9
-8	10
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-25	26
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-27	28
+IRS2_HUMAN	JAK3_HUMAN
+JAK3_HUMAN	VILI_HUMAN
+IL2RG_HUMAN	ETS1_HUMAN
+AKT1_HUMAN	P85A_HUMAN
+P85B_HUMAN	IRS1_HUMAN
+Q14342_HUMAN	JAK1_HUMAN
+IRS1_HUMAN	L7RT18_HUMAN
+P85B_HUMAN	Q14342_HUMAN
+L7RRS6_HUMAN	JAK1_HUMAN
+SHB_HUMAN	IL2RG_HUMAN
+P85B_HUMAN	SHC1_HUMAN
+SHC1_HUMAN	CBL_HUMAN
+PK3CA_HUMAN	IRS2_HUMAN
+IRS1_HUMAN	PK3CA_HUMAN
+STAM1_HUMAN	JAK1_HUMAN
+SOS1_HUMAN	AKT1_HUMAN
+IRS2_HUMAN	P85A_HUMAN
+SHB_HUMAN	GAB1_HUMAN
+IRS2_HUMAN	JAK1_HUMAN
+JAK1_HUMAN	SHC1_HUMAN
+ETS1_HUMAN	GCR_HUMAN
+PK3CA_HUMAN	PK3CG_HUMAN
+JAK3_HUMAN	JAK1_HUMAN
+PK3CA_HUMAN	P85B_HUMAN
+Q14342_HUMAN	A1L4K2_HUMAN
+PTN11_HUMAN	AKT1_HUMAN
+CBL_HUMAN	L7RT18_HUMAN
+PTN11_HUMAN	GAB1_HUMAN
+IL2RG_HUMAN	JAK1_HUMAN
+GAB1_HUMAN	PK3CA_HUMAN
+JAK3_HUMAN	CBL_HUMAN
+SOS1_HUMAN	P85B_HUMAN
+SHC1_HUMAN	IL2RG_HUMAN
+PTN11_HUMAN	SOS1_HUMAN
+JAK3_HUMAN	IL2RG_HUMAN
+CRKL_HUMAN	SHC1_HUMAN
+GAB1_HUMAN	P85B_HUMAN
+IRS1_HUMAN	IRS2_HUMAN
+P85A_HUMAN	IRS1_HUMAN
+L7RRS6_HUMAN	GCR_HUMAN
+JAK1_HUMAN	SOS1_HUMAN
+PK3CA_HUMAN	PTN11_HUMAN
+IL2RG_HUMAN	L7RRS6_HUMAN
+IRS2_HUMAN	PTN11_HUMAN
+CRKL_HUMAN	PTN11_HUMAN
+PTN11_HUMAN	Q14342_HUMAN
+STA5B_HUMAN	NMI_HUMAN
+PTN11_HUMAN	IRS1_HUMAN
+PK3CG_HUMAN	P85B_HUMAN
+IL2RG_HUMAN	SOS1_HUMAN
+JAK3_HUMAN	PTN11_HUMAN
+L7RRS6_HUMAN	HS90A_HUMAN
+SHC1_HUMAN	A1L4K2_HUMAN
+P85A_HUMAN	P85B_HUMAN
+Q14342_HUMAN	PK3CA_HUMAN
+IRS1_HUMAN	CBL_HUMAN
+PK3CA_HUMAN	SOS1_HUMAN
+GAB1_HUMAN	L7RT18_HUMAN
+GAB1_HUMAN	AKT1_HUMAN
+P85A_HUMAN	L7RRS6_HUMAN
+Q14342_HUMAN	IL2RG_HUMAN
+IL2RG_HUMAN	IRS2_HUMAN
+P85A_HUMAN	JAK1_HUMAN
+JAK3_HUMAN	AKT1_HUMAN
+CRKL_HUMAN	L7RT18_HUMAN
+SOS1_HUMAN	L7RT18_HUMAN
+AKT1_HUMAN	HS90A_HUMAN
+L7RT18_HUMAN	IRS2_HUMAN
+IL2RG_HUMAN	PK3CA_HUMAN
+GAB1_HUMAN	CRKL_HUMAN
+A1L4K2_HUMAN	GCR_HUMAN
+CRKL_HUMAN	P85A_HUMAN
+P85B_HUMAN	CBL_HUMAN
+SHC1_HUMAN	IRS1_HUMAN
+CRKL_HUMAN	STA5B_HUMAN
+SOS1_HUMAN	L7RRS6_HUMAN
+JAK3_HUMAN	ETS1_HUMAN
+JAK3_HUMAN	IRS1_HUMAN
+IL2RG_HUMAN	IRS1_HUMAN
+CRKL_HUMAN	PK3CA_HUMAN
+GAB1_HUMAN	P85A_HUMAN
+STA5B_HUMAN	GCR_HUMAN
+CBL_HUMAN	STA5B_HUMAN
+JAK3_HUMAN	L7RRS6_HUMAN
+HS90A_HUMAN	Q14342_HUMAN
+CRKL_HUMAN	SOS1_HUMAN
+IL2RG_HUMAN	PTN11_HUMAN
+P85A_HUMAN	PK3CA_HUMAN
+P85B_HUMAN	CRKL_HUMAN
+STAM1_HUMAN	JAK3_HUMAN
+A1L4K2_HUMAN	P85A_HUMAN
+GAB1_HUMAN	A1L4K2_HUMAN
+SHB_HUMAN	L7RT18_HUMAN
+P85A_HUMAN	Q14342_HUMAN
+SHC1_HUMAN	PTN11_HUMAN
+PTN11_HUMAN	L7RRS6_HUMAN
+PK3CG_HUMAN	GAB1_HUMAN
+IRS2_HUMAN	SHC1_HUMAN
+HS90A_HUMAN	GCR_HUMAN
+Q14342_HUMAN	JAK3_HUMAN
+L7RT18_HUMAN	P85A_HUMAN
+SHB_HUMAN	JAK3_HUMAN
+IRS1_HUMAN	SOS1_HUMAN
+JAK1_HUMAN	PK3CA_HUMAN
+A1L4K2_HUMAN	IRS1_HUMAN
+SHB_HUMAN	PK3CA_HUMAN
+Q14342_HUMAN	IRS1_HUMAN
+PTN11_HUMAN	P85A_HUMAN
+IL2RG_HUMAN	AKT1_HUMAN
+GAB1_HUMAN	SOS1_HUMAN
+SHB_HUMAN	P85A_HUMAN
+CBL_HUMAN	PK3CA_HUMAN
+JAK3_HUMAN	PK3CA_HUMAN
+PTN11_HUMAN	CBL_HUMAN
+CRKL_HUMAN	A1L4K2_HUMAN
+STA5B_HUMAN	ETS1_HUMAN
+L7RRS6_HUMAN	Q14342_HUMAN
+CRKL_HUMAN	CBL_HUMAN
+GAB1_HUMAN	SHC1_HUMAN
+SHC1_HUMAN	SOS1_HUMAN
+A1L4K2_HUMAN	L7RT18_HUMAN
+PK3CA_HUMAN	L7RRS6_HUMAN
+JAK1_HUMAN	IRS1_HUMAN
+JAK1_HUMAN	AKT1_HUMAN
+PK3CA_HUMAN	A1L4K2_HUMAN
+L7RT18_HUMAN	PK3CA_HUMAN
+SHC1_HUMAN	AKT1_HUMAN
+IRS1_HUMAN	CRKL_HUMAN
+L7RT18_HUMAN	SHC1_HUMAN
+CBL_HUMAN	P85A_HUMAN
+SHC1_HUMAN	L7RRS6_HUMAN
+JAK1_HUMAN	ETS1_HUMAN
+JAK3_HUMAN	P85A_HUMAN
+SOS1_HUMAN	Q14342_HUMAN
+IL2RG_HUMAN	CBL_HUMAN
+IL2RG_HUMAN	P85A_HUMAN
+PK3CA_HUMAN	AKT1_HUMAN
+AKT1_HUMAN	IRS1_HUMAN
+L7RT18_HUMAN	STA5B_HUMAN
+JAK3_HUMAN	SOS1_HUMAN
+PTN11_HUMAN	A1L4K2_HUMAN
+IRS2_HUMAN	P85B_HUMAN
+PK3CA_HUMAN	SHC1_HUMAN
+Q14342_HUMAN	SHC1_HUMAN
+PTN11_HUMAN	STA5B_HUMAN
+GCR_HUMAN	Q14342_HUMAN
+GAB1_HUMAN	IRS2_HUMAN
+PTN11_HUMAN	JAK1_HUMAN
+Q14342_HUMAN	L7RT18_HUMAN
+Q14342_HUMAN	CBL_HUMAN
+JAK3_HUMAN	SHC1_HUMAN
+JAK1_HUMAN	CBL_HUMAN
+AKT1_HUMAN	L7RRS6_HUMAN
+SHC1_HUMAN	STA5B_HUMAN
+SHB_HUMAN	JAK1_HUMAN
+P85A_HUMAN	SOS1_HUMAN
+CBL_HUMAN	SOS1_HUMAN
+SHC1_HUMAN	P85A_HUMAN
+PTN11_HUMAN	PK3CG_HUMAN