init

Author: murphycj

README.md

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+# Visualize Gene Fusion (VGFusion)
+Python package providing that can visualize different annotations of a gene fusion.

__init__.py

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+import argparse
+
+from vgfusion import *
+
+parser = argparse.ArgumentParser(description='Visualize Gene Fusion (VGFusion)')
+parser.add_argument(
+    '--gene5prime',
+    type=str,
+    required=True,
+    help='5\' gene partner'
+)
+parser.add_argument(
+    '--gene3prime',
+    type=str,
+    required=True,
+    help='3\' gene partner'
+)
+parser.add_argument(
+    '--5primeLocation',
+    type=str,
+    required=True,
+    help='Genomic location of predicted fuins for the 5\' gene partner'
+)
+parser.add_argument(
+    '--3primeLocation',
+    type=str,
+    required=True,
+    help='Genomic location of predicted fuins for the 3\' gene partner'
+)
+parser.add_argument(
+    '--ref',
+    type=str,
+    required=True,
+    help='Reference genome (GRCh38, GRCh37, or GRCm38)'
+)
+parser.add_argument(
+    '--database',
+    type=str,
+    required=False,
+    default=None,
+    help='Path to database. If not specified VGFusion will make RESTful API calls to Ensembl instead'
+)
+parser.add_argument(
+    '--type',
+    type=str,
+    required=False,
+    default='png',
+    help='Image file type (png, jpeg, pdf). Default: png'
+)
+parser.add_argument(
+    '--scale',
+    type=int,
+    required=False,
+    default=-1,
+    help='Length in amino acids to scale the gene fusion image (default: max length of fusion product)'
+)
+parser.add_argument(
+    '--WT',
+    action='store_true',
+    required=False,
+    help='Include this to plot wild-type architechtures of the 5\' and 3\' genes'
+)
+
+args = parser.parse_args()
+
+main(args=args)

bin/build_database.py

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+import os
+from setuptools import setup, find_packages
+
+README = open('README.md').read()
+
+setup(
+    version = 0.1,
+    name='vgfusion',
+    packages = find_packages(),
+    description = "Python package providing that can visualize different annotations of a gene fusion.",
+    author='Charles Murphy',
+    license='Non-commercial',
+    long_description=README
+)

bin/vgfusion.py

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+from vgfusion import *

setup.py

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+
+class Gene:
+    """
+    Stores the necessary information to specify the architecture of either
+    wild-type genes or fusion gene.
+    """
+
+    def __init__(self):
+        self.gene_5prime=''
+        self.gene_5prime_junction=0
+
+        self.gene_3prime=''
+        self.gene_3prime_junction=0

vgfusion/__init__.py

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+"""
+Functions to plot the gene fusions
+"""
+
+from PIL import *

vgfusion/database.py

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+import sys
+import requests
+
+def main(args):
+
+
+    if args.database is not None:
+        import tinydb
+
+