v0.8.7

conda.recipe/meta.yaml

@@ -1,6 +1,3 @@
-
-#{% set name = "vcf2gwas" %}
-#{% set version = "0.6.4" %}
 {% set data = load_setup_py_data() %}
 
 package:
@@ -9,61 +6,35 @@ package:
 
 source:
   git_url: https://github.com/frankvogt/vcf2gwas.git
-  # url: https://github.com/frankvogt/vcf2gwas/releases/download/{{ version }}/vcf2gwas-{{ version }}.tar.gz
 
 build:
-  # If the installation is complex, or different between Unix and Windows, use
-  # separate bld.bat and build.sh files instead of this key.  Add the line
-  # "skip: True  # [py<35]" (for example) to limit to Python 3.5 and newer, or
-  # "skip: True  # [not win]" to limit to Windows.
   number: 0
   script: "{{ PYTHON }} -m pip install . -vv"
-  # script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv .
   noarch: python
 
   entry_points:
-    # - vcf2gwas = vcf2gwas.__main__:main
-    # - install_vcf2gwas = vcf2gwas.install:main
     {% for entry in data['entry_points']['console_scripts'] %}
       - {{ entry.split('=')[0].strip() }} = {{ entry.split('=')[1].strip() }}
     {% endfor %}
 
 
 requirements:
-  # if you need compilers, uncomment these
-  #    read more at https://docs.conda.io/projects/conda-build/en/latest/resources/compiler-tools.html
-  # build:
-  #   - {{ compilers('c') }}
   host:
     - python==3.9
     - pip
 
   run:
     - python==3.9
 
-
-    # dependencies are defined in setup.py
     {% for dep in data['install_requires'] %}
     - {{ dep.lower() }}
     {% endfor %}
-    #{# raw is for ignoring templating with cookiecutter, leaving it for use with conda-build #}
 
 test:
-  #source_files:
-    #- tests
-  #requires:
-    #- pytest
-    #- pytest-cov
-  #imports:
-  #  - utils.py
-  #  - parsing.py
-  #commands:
-  #  - test_vcf2gwas
 
 about:
   home: https://github.com/frankvogt/vcf2gwas
   summary: Python API for comprehensive GWAS analysis using GEMMA
-  license: GNUv3
-  #license: {{ data.get('license') }}
+  license: {{ data.get('license') }}
   license_file: LICENSE
   dev_url: https://github.com/frankvogt/vcf2gwas

setup.py

@@ -17,7 +17,7 @@
 
 setup(
     name='vcf2gwas',
-    version='0.8.6',
+    version='0.8.7',
     description="Python API for comprehensive GWAS analysis using GEMMA",
     license="GNUv3",
     author="Frank Vogt",

vcf2gwas/install.py

@@ -1,4 +1,3 @@
-import subprocess
 import os
 import shutil
 
@@ -22,16 +21,7 @@
 """
 
 def main():
-    #print("Checking environment.. \nUpdating dependencies..")
-    #env_name = os.environ["CONDA_DEFAULT_ENV"]
-    #subprocess.run(["conda", "env", "update", "-n", env_name, "-f", os.path.join(os.path.dirname(__file__), 'environment.yml')])
-    #try:
-    #    #subprocess.run(["pip", "install", "umap-learn"])
-    #    subprocess.run(["conda", "env", "create", "-f",
-    #        os.path.join(os.path.dirname(__file__), 'environment.yml')])
-    #except Exception as e:
-    #    print(e)
-    #print("Environment is now up to date")
+
     print("Copying example input files to current working directory..")
     try:
         os.mkdir("input")
@@ -43,4 +33,3 @@ def main():
     print("Copying README and LICENSE files..")
     shutil.copy(os.path.join(os.path.dirname(__file__), 'README.pdf'), 'README.pdf')
     shutil.copy(os.path.join(os.path.dirname(__file__), 'LICENSE'), 'LICENSE')
-    #print("Installation complete\n")

vcf2gwas/parsing.py

@@ -31,7 +31,7 @@
     from psutil import virtual_memory
 
 def set_version_number():
-    return "0.8.6"
+    return "0.8.7"
 
 def getArgs(argv=None):
     """Description:

vcf2gwas/utils.py

@@ -19,7 +19,8 @@
 along with vcf2gwas.  If not, see <https://www.gnu.org/licenses/>.
 """
 
-from vcf2gwas.parsing import Parser
+#from vcf2gwas.parsing import Parser
+from parsing import *
 
 import os
 import subprocess
@@ -80,9 +81,7 @@
 
 from parsing import *
 
-sns.set_style('white')
-#sns.set_style('ticks')
-#os.chdir(os.path.dirname(os.path.abspath(__file__)))
+sns.set_theme(style='white', palette='deep')
 
 #set fontsize
 argvals = None
@@ -99,7 +98,6 @@
 plt.rc('axes', linewidth=fontsize5)
 plt.rc('xtick.major', width=fontsize5, size=fontsize4)
 plt.rc('ytick.major', width=fontsize5, size=fontsize4)
-sns.set_color_codes()
 
 ############################## Functions ##############################
 
@@ -1605,7 +1603,7 @@ def format_data(prefix, case, pcol, path, sep='\t', chromosome='chr'):
         data_grouped = data.groupby((chromosome))
         return data, data_grouped
 
-    def manh_plot(df, Log, prefix, pcol, path, sigval, x, nolabel, colors = ['#E24E42', '#008F95'], refSNP = False):
+    def manh_plot(df, Log, prefix, pcol, path, sigval, x, nolabel, colors = ['#4C72B0', '#C44E52'], refSNP = False):
         """Description:
         creates manhattan plot from prepared dataframe and saves plot
         based on: https://github.com/Pudkip/Pyhattan/blob/master/Pyhattan/__init__.py"""
@@ -2759,4 +2757,4 @@ def rangeTrans(y):
         return (y - np.nanmin(y))/(np.nanmax(y) - np.nanmin(y))
 
     def standTrans(y):
-        return (y - np.nanmean(y))/np.nanstd(y, ddof=1)
+        return (y - np.nanmean(y))/np.nanstd(y, ddof=1)