Merge pull request #25 from rhshah/SupportForLatestPandas

Support for latest pandas
rhshah · May 24, 2019 · 7d59154 · 7d59154
2 parents 3b6ada3 + 9737013
commit 7d59154
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Showing 6 changed files with 105 additions and 15 deletions.
diff --git a/.gitignore 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
diff --git a/README.rst b/README.rst
@@ -44,7 +44,7 @@ Required Packages
 =================
 We require that you install:
 
-:pandas: `v0.16.2 <http://pandas.pydata.org/>`_
+:pandas: `v0.24.2 <http://pandas.pydata.org/>`_
 :biopython: `v1.65 <http://biopython.org/wiki/Main_Page>`_
 :Pillow: `v3.4.2 <https://pypi.python.org/pypi/Pillow/3.4.2>`_
 :reportlab: `v3.3.0 <https://pypi.python.org/pypi/reportlab/3.3.0>`_

diff --git 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):
@@ -220,7 +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/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
@@ -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
@@ -38,11 +38,11 @@ def read(*filenames, **kwargs):
       packages=['iAnnotateSV'],
       install_requires=[
           'numpy==1.14.0',
-          'openpyxl==1.8.6',
-          'pandas==0.16.2',
+          'openpyxl==2.4.0',
+          'pandas==0.24.2',
           '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'
         ),
-      )
+      )