Initial Import

CONTRIBUTING.md

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+Contributing to graph-imputation-match
+===
+
+1) Log into Github web interface with your username-nmdp account
+
+2) Browse to the repo at https://github.com/nmdp-bioinformatics/graph-imputation-match, hit the Fork button
+
+3) Copy the clone URL from the Github web page for the fork (something like https://github.com/username-nmdp/graph-imputation-match.git)
+
+4) Clone the fork
+```bash
+$ git clone https://github.com/username-nmdp/graph-imputation-match.git
+$ cd graph-imputation-match
+```
+
+5) Add upstream as remote
+```bash
+$ git remote add upstream https://github.com/nmdp-bioinformatics/graph-imputation-match
+```
+
+6) Pull and merge latest changes from upstream master to your local master branch
+```bash
+$ git checkout master
+$ git pull upstream master
+$ git push
+```
+
+7) Create a new local feature branch
+```bash
+$ git checkout -b new-feature-branch
+```
+
+8) Edit files locally
+
+9) Commit changes to local feature branch
+```bash
+$ git commit -m "made changes"
+```
+
+10) Push changes from local feature branch to remote feature branch on your fork
+```bash
+$ git push origin new-feature-branch
+```
+
+11) Browse to the Github web page for your fork repo (something like https://github.com/username-nmdp/graph-imputation-match) and hit the new pull request button
+
+12) Edit the pull request description and hit save (or create or new, I can't remember) button
+
+13) Other contributors will review the changes in the pull request
+
+14) When the pull request looks good, it is merged into the upstream repo
+
+15) Hit the delete branch button to delete your remote feature branch (the commits have been merge upstream, so it is no longer necessary)
+
+16) Delete your local feature branch
+```bash
+$ git branch -d new-feature-branch
+```

LICENSE

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+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
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+other than an Application or a Combined Work as defined below.
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README.md

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+#  GRIMM: Graph IMputation and Matching for HLA Genotypes
+
+Graph-based imputation and matching, a.k.a. new imputation method (NIM).
+
+| Subdirectory    | Description |
+| :-------------- | :---------- |
+| graph_generator | Python code to generate (haplotype frequency) CSV files which can be imported into Neo4j |
+| gl_impute       | old Python code for graph-based imputation.  Still needed for cypher queries (?) |
+| multi_race_ipute | Python code for graph-based imputation |
+| validation      | Code for validation of components of this repository |
+
+# Walkthrough
+
+### 1. Generate Initial Graph
+ Follow [Graph Generation](graph_generator/README.md) to generate haplotype frequency CSV files and import to Neo4j.
+
+
+### 2. Perform Imputation
+ Follow [Imputation](multi_race_impute/README.md) directions to produce imputation results from frequency files.
+
+
+### 3. Perform Matching
+  Follow [Match Validation](matching/README.md) to perform matching and compare against consensus results.

gl_impute/Makefile

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+init:
+	pip install -r requirements.txt
+	pip install git+https://github.com/bmilius-nmdp/pyglstring.git
+
+test:
+	nosetests -v tests
+
+install:
+	python setup.py install
+
+upgrade:
+	pip install . --upgrade
+
+clean:
+	pip uninstall gl-impute
+	python setup.py clean --all
+
+examples:
+	python -m doctest -v examples.rst

gl_impute/bin/Run_File

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+from py2neo import Graph
+from impute import Imputation
+import inspect
+import os
+import json
+
+#fname='/home/yoram/gl_impute/don.missing-weps.txt'
+fname='mytest.txt'
+
+json_file = 'yoram.json'
+config_data = open(json_file).read()
+credentials = json.loads(config_data)
+
+graph = Graph(credentials["graph"], user=credentials["user"], password=credentials["password"])
+test=Imputation(graph)
+test.impute_file(fname)

gl_impute/bin/impute_file.py

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+""" docstring for module """
+import argparse  # for command line arguments
+from py2neo import Graph
+from impute.impute import Imputation
+import json
+
+
+def main():
+    """This is run if file is directly executed, but not if imported as
+    module. Having this in a separate function  allows importing the file
+    into interactive python, and still able to execute the
+    function for testing"""
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-f", "--file",
+                        required=True,
+                        help="Input file",
+                        type=str)
+
+    parser.add_argument("-l", "--url",
+                        default="http://localhost:7474/data/",
+                        help="URL for neo4j database - Default ",
+                        type=str)
+
+    parser.add_argument("-u", "--user",
+                        default="neo4j",
+                        help="Username for neo4j database",
+                        type=str)
+
+    parser.add_argument("-p", "--password",
+                        default="new",
+                        help="Password for neo4j database",
+                        type=str)
+
+    parser.add_argument("-e", "--epsilon",
+                        help="Epsilion used for trimming",
+                        default=0.5,
+                        type=float)
+
+    parser.add_argument("-c", "--config",
+                        help="Option for providing configuration file",
+                        type=str)
+
+    parser.add_argument("-v", "--verbose",
+                        help="Option for running in verbose",
+                        default=False,
+                        type=bool)
+
+    args = parser.parse_args()
+    inputfile = args.file
+    epsilon = args.epsilon
+    config = args.config
+    password = args.password
+    user = args.user
+    verbose = args.verbose
+
+    if(config):
+        config_data = open(config).read()
+        credentials = json.loads(config_data)
+        password = credentials['password']
+        user = credentials['user']
+
+    # Create a new neo4j graph object with py2neo
+    graph = Graph(args.url, user=user, password=password)
+
+    # Create a new imutation object
+    # This object is what made with Yoram's code
+    imp = Imputation(graph, verbose)
+    inputdata = (l.strip() for l in open(inputfile, "r") if l.strip())
+
+    for line in inputdata:
+        line.rstrip()
+        line.strip('\n')
+        [subid, glstring] = line.split("%")
+        res = imp.comp_cand(glstring, epsilon)
+        len_res = len(res['Haps'])
+        for i in range(len_res):
+            print(subid, "^".join(res['Haps'][i]), res['Probs'][i])
+
+
+if __name__ == '__main__':
+    """The following will be run if file is executed directly,
+    but not if imported as a module"""
+    main()