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AthenACHY · May 21, 2018 · 77c01ae · 77c01ae
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diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,4 @@
+include README.md
+recursive-include SplitFusion/ *.py
+recursive-include SplitFusion/Reference_feat/ *.txt
+
diff --git a/SplitFusion.egg-info/PKG-INFO b/SplitFusion.egg-info/PKG-INFO
@@ -0,0 +1,12 @@
+Metadata-Version: 1.0
+Name: SplitFusion
+Version: 0.0
+Summary: UNKNOWN
+Home-page: UNKNOWN
+Author: UNKNOWN
+Author-email: UNKNOWN
+License: Creative Commons Attribution-Noncommercial-Share Alike license
+Description-Content-Type: UNKNOWN
+Description: SplitFusion
+
+Platform: UNKNOWN
diff --git a/SplitFusion.egg-info/SOURCES.txt b/SplitFusion.egg-info/SOURCES.txt
@@ -0,0 +1,15 @@
+MANIFEST.in
+README.md
+setup.py
+SplitFusion/2018_05_21_SplitFusion.py
+SplitFusion/Fusion_annotation.py
+SplitFusion/Group_split.py
+SplitFusion/Multiple_alignment.py
+SplitFusion/__init__.py
+SplitFusion.egg-info/PKG-INFO
+SplitFusion.egg-info/SOURCES.txt
+SplitFusion.egg-info/dependency_links.txt
+SplitFusion.egg-info/requires.txt
+SplitFusion.egg-info/top_level.txt
+SplitFusion/Reference_feat/NCBIRef_seq_HG19_fest.txt
+SplitFusion/Reference_feat/NCBI_refSeqGRC38_features.txt
diff --git a/SplitFusion.egg-info/dependency_links.txt b/SplitFusion.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/SplitFusion.egg-info/requires.txt b/SplitFusion.egg-info/requires.txt
@@ -0,0 +1,3 @@
+subprocess32==3.2.7
+HTSeq==0.9.1
+statsmodels==0.8.0
diff --git a/SplitFusion.egg-info/top_level.txt b/SplitFusion.egg-info/top_level.txt
@@ -0,0 +1 @@
+SplitFusion
diff --git a/Split_Fusion/2018_05_21_SplitFusion.py → SplitFusion/2018_05_21_SplitFusion.py b/Split_Fusion/2018_05_21_SplitFusion.py → SplitFusion/2018_05_21_SplitFusion.py
diff --git a/Split_Fusion/Fusion_annotation.py → SplitFusion/Fusion_annotation.py b/Split_Fusion/Fusion_annotation.py → SplitFusion/Fusion_annotation.py
diff --git a/Split_Fusion/Group_split.py → SplitFusion/Group_split.py b/Split_Fusion/Group_split.py → SplitFusion/Group_split.py
@@ -85,12 +85,16 @@ def collect_reads_from_splits(a_split_list, breakpoints):
 def group_splits_reads(reads, SA_bundles):
     """summarize splits and leave an example per split for annotation """
     """assume same left-right_split, same overlaps and gaps number in read"""
+    """remove split_location_that fused to more than 20 different places -- potential artefacts???"""
     left_right_splits={}
     for r in reads:
         match_cood=SA_bundles[r][1]
         boundary="-".join(["_".join([str(x) for x in SA_bundles[r][1][0][2]]), "_".join([str(x) for x in SA_bundles[r][1][-1][0]])])
         left_right_splits[boundary]=match_cood
-    return left_right_splits
+    if len(left_right_splits)<=20:
+        return left_right_splits
+    else:
+        return {}
 
 def combine_left_right_clusteres(left_splits_clustered0, right_splits_clustered0, SA_bundles, left_breakpoints, right_breakpoints):
     """remove redundancy of splits invovled in multiple fusions"""

diff --git a/Split_Fusion/Multiple_alignment.py → SplitFusion/Multiple_alignment.py b/Split_Fusion/Multiple_alignment.py → SplitFusion/Multiple_alignment.py
diff --git a/Reference_feat/NCBIRef_seq_HG19_fest.txt → .../Reference_feat/NCBIRef_seq_HG19_fest.txt b/Reference_feat/NCBIRef_seq_HG19_fest.txt → .../Reference_feat/NCBIRef_seq_HG19_fest.txt
diff --git a/Reference_feat/NCBI_refSeqGRC38_features.txt → ...erence_feat/NCBI_refSeqGRC38_features.txt b/Reference_feat/NCBI_refSeqGRC38_features.txt → ...erence_feat/NCBI_refSeqGRC38_features.txt
diff --git a/SplitFusion/__init__.py b/SplitFusion/__init__.py
diff --git a/dist/SplitFusion-0.0.tar.gz b/dist/SplitFusion-0.0.tar.gz
diff --git a/setup.py b/setup.py
@@ -0,0 +1,24 @@
+##packaging command python setup.py sdist
+
+import sys
+import os.path
+from setuptools import setup, Extension, find_packages
+
+
+setup(
+    name='SplitFusion',
+    version='0.0',
+    packages=find_packages(),
+    license='Creative Commons Attribution-Noncommercial-Share Alike license',
+    long_description=open('README.md').read(),
+    package_dir = {'SplitFusion': 'SplitFusion/'},
+    package_data={'ReferenceGenomes': ['Reference_feat/*.txt']},
+    py_modules = ['SplitFusion.Multiple_alignment', 'SplitFusion.Fusion_annotation', 'SplitFusion.Group_split'],
+    install_requires=['subprocess32==3.2.7' ,
+                        'HTSeq==0.9.1',
+                        'statsmodels==0.8.0'],
+    include_package_data=True
+
+)
+
+