From 2c7eccfab31ecd1fab49d31c2e019cd2e41793c4 Mon Sep 17 00:00:00 2001 From: Ronak Date: Fri, 24 May 2019 17:25:20 -0400 Subject: [PATCH 1/3] Update AnnotationForKinaseDomain.py --- iAnnotateSV/AnnotationForKinaseDomain.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/iAnnotateSV/AnnotationForKinaseDomain.py b/iAnnotateSV/AnnotationForKinaseDomain.py index d712305..098b77c 100644 --- a/iAnnotateSV/AnnotationForKinaseDomain.py +++ b/iAnnotateSV/AnnotationForKinaseDomain.py @@ -9,33 +9,34 @@ import logging import coloredlogs import re +import helper as hp coloredlogs.install(level='DEBUG') def run(svDFA, refPath, ctPath, allctPath, upPath, verbose): if(os.path.isfile(upPath)): - upDF = pd.read_table(upPath, sep="\t") + upDF = hp.ReadFile(upPath) else: if(verbose): logging.critical( "iAnnotateSV::AnnotationForKinaseDomain: Location of Uniprot Annoation file is incorrect!!!") sys.exit(1) if(os.path.isfile(ctPath)): - ctDF = pd.read_table(ctPath, sep="\t") + ctDF = hp.ReadFile(ctPath) else: if(verbose): logging.warn( "iAnnotateSV::AnnotationForKinaseDomain: Location of assay specific canonical transcript file is incorrect!!!") ctDF = pd.DataFrame() if(os.path.isfile(allctPath)): - allctDF = pd.read_table(allctPath, sep="\t") + allctDF = hp.ReadFile(allctPath) else: if(verbose): logging.critical( "iAnnotateSV::AnnotationForKinaseDomain: Location of all canonical transcript file is incorrect!!!") sys.exit(1) if(os.path.isfile(refPath)): - refDF = pd.read_table(refPath, sep="\t") + refDF = hp.ReadFile(refPath) refDF.columns = refDF.columns.str.replace('#', '') else: if(verbose): From 84c6b5c769010dc765c51e81447e1739f4391b8c Mon Sep 17 00:00:00 2001 From: Ronak Date: Fri, 24 May 2019 17:30:01 -0400 Subject: [PATCH 2/3] Adding Pandas changes --- .gitignore | 89 ++++++++++++++++++++++++ iAnnotateSV/AnnotationForKinaseDomain.py | 2 +- setup.py | 8 +-- 3 files changed, 94 insertions(+), 5 deletions(-) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a0ad585 --- /dev/null +++ b/.gitignore @@ -0,0 +1,89 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# IPython Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# dotenv +.env + +# virtualenv +venv/ +ENV/ + +# Spyder project settings +.spyderproject + +# Rope project settings +.ropeproject \ No newline at end of file diff --git a/iAnnotateSV/AnnotationForKinaseDomain.py b/iAnnotateSV/AnnotationForKinaseDomain.py index 098b77c..26218cd 100644 --- a/iAnnotateSV/AnnotationForKinaseDomain.py +++ b/iAnnotateSV/AnnotationForKinaseDomain.py @@ -221,7 +221,7 @@ def getKinaseInfo(chrom, pos, gene, egene1, egene2, transcript, refDF, upDF): else: kanno = "Kinase Domain Not Included" else: - if(chromEnd <= pos1): + if(chromEnd <= pos): if(pos <= chromStart): kanno = "Partial Kinase Domain Included" else: diff --git a/setup.py b/setup.py index 7f64552..0c9c219 100755 --- a/setup.py +++ b/setup.py @@ -38,11 +38,11 @@ def read(*filenames, **kwargs): packages=['iAnnotateSV'], install_requires=[ 'numpy==1.14.0', - 'openpyxl==1.8.6', + 'openpyxl==2.4.0', 'pandas==0.16.2', 'nose==1.3.7', - 'codecove==2.0.5', - 'coverage==4.3.4' + 'codecov==2.0.5', + 'coverage==4.3.4', 'pillow==3.4.2', 'biopython==1.65', 'reportlab==3.3.0', @@ -58,4 +58,4 @@ def read(*filenames, **kwargs): 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Development Status :: 3' ), - ) \ No newline at end of file + ) From 973701326edf284a37d8ae456df1cda318200f2f Mon Sep 17 00:00:00 2001 From: Ronak Date: Fri, 24 May 2019 17:42:16 -0400 Subject: [PATCH 3/3] Changing Versions --- README.rst | 2 +- iAnnotateSV/__init__.py | 4 ++-- requirements.txt | 4 ++-- setup.py | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/README.rst b/README.rst index a913d8a..5eee0f1 100755 --- a/README.rst +++ b/README.rst @@ -44,7 +44,7 @@ Required Packages ================= We require that you install: -:pandas: `v0.16.2 `_ +:pandas: `v0.24.2 `_ :biopython: `v1.65 `_ :Pillow: `v3.4.2 `_ :reportlab: `v3.3.0 `_ diff --git a/iAnnotateSV/__init__.py b/iAnnotateSV/__init__.py index 27d0d69..72ba806 100755 --- a/iAnnotateSV/__init__.py +++ b/iAnnotateSV/__init__.py @@ -1,6 +1,6 @@ __title__ = 'iAnnotateSV' -__version__ = '1.0.9' +__version__ = '1.1.0' __author__ = 'Ronak H Shah' __license__ = 'Apache Software License' -__copyright__ = 'Copyright 2018 Ronak Hasmukh Shah' +__copyright__ = 'Copyright 2019 Ronak Hasmukh Shah' diff --git a/requirements.txt b/requirements.txt index cee1817..bd4205b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ numpy==1.14.0 -openpyxl==1.8.6 +openpyxl==2.4.0 nose==1.3.7 -pandas==0.16.2 +pandas==0.24.2 coloredlogs==5.2 codecov==2.0.5 coverage==4.3.4 diff --git a/setup.py b/setup.py index 0c9c219..617c112 100755 --- a/setup.py +++ b/setup.py @@ -39,7 +39,7 @@ def read(*filenames, **kwargs): install_requires=[ 'numpy==1.14.0', 'openpyxl==2.4.0', - 'pandas==0.16.2', + 'pandas==0.24.2', 'nose==1.3.7', 'codecov==2.0.5', 'coverage==4.3.4',