RefgenDetector 3.0.0__tar.gz → 3.0.2__tar.gz

{refgendetector-3.0.0/src/RefgenDetector.egg-info → refgendetector-3.0.2}/PKG-INFO

@@ -1,7 +1,6 @@
 Metadata-Version: 2.4
 Name: RefgenDetector
-Version: 3.0.0
-Summary: RefgenDetector
+Version: 3.0.2
 Author: Mireia Marin i Ginestar
 Author-email: <mireia.marin@crg.eu>
 Keywords: python
@@ -9,13 +8,13 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: Unix
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: argparse
 Requires-Dist: pysam
 Requires-Dist: psutil
 Requires-Dist: rich
 Requires-Dist: pandas
 Requires-Dist: dnspython
 Requires-Dist: msgpack
+Requires-Dist: numpy
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -24,7 +23,6 @@ Dynamic: description-content-type
 Dynamic: keywords
 Dynamic: license-file
 Dynamic: requires-dist
-Dynamic: summary
 
 # EGA - RefgenDetector
 

{refgendetector-3.0.0 → refgendetector-3.0.2}/setup.py

@@ -1,32 +1,31 @@
 from setuptools import setup, find_packages
-# read the contents of your README file
 from pathlib import Path
+
 this_directory = Path(__file__).parent
 long_description = (this_directory / "README.md").read_text()
 
-VERSION = '3.0.0'
+VERSION = '3.0.2'
 DESCRIPTION = 'RefgenDetector'
 
-# Setting up
 setup(
     name="RefgenDetector",
     version=VERSION,
     author="Mireia Marin i Ginestar",
     author_email="<mireia.marin@crg.eu>",
-    description=DESCRIPTION,
     long_description=long_description,
     long_description_content_type='text/markdown',
-    install_requires=['argparse', 'pysam', 'psutil', 'rich', 'pandas', 'dnspython', 'msgpack'],
+    install_requires=['pysam', 'psutil', 'rich', 'pandas', 'dnspython', 'msgpack', 'numpy'],
     keywords=['python'],
     classifiers=[
         "Programming Language :: Python :: 3",
-        "Operating System :: Unix"],
+        "Operating System :: Unix",
+    ],
     entry_points={
         'console_scripts': [
             'refgenDetector=refgenDetector.refgenDetector_main:main',
         ],
     },
     packages=find_packages(where='src'),
-    package_dir={'': 'src'}
-
+    package_dir={'': 'src'},
+    package_data={"refgenDetector": ["*.msgpack"]}
 )

{refgendetector-3.0.0 → refgendetector-3.0.2/src/RefgenDetector.egg-info}/PKG-INFO

@@ -1,7 +1,6 @@
 Metadata-Version: 2.4
 Name: RefgenDetector
-Version: 3.0.0
-Summary: RefgenDetector
+Version: 3.0.2
 Author: Mireia Marin i Ginestar
 Author-email: <mireia.marin@crg.eu>
 Keywords: python
@@ -9,13 +8,13 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: Unix
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: argparse
 Requires-Dist: pysam
 Requires-Dist: psutil
 Requires-Dist: rich
 Requires-Dist: pandas
 Requires-Dist: dnspython
 Requires-Dist: msgpack
+Requires-Dist: numpy
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -24,7 +23,6 @@ Dynamic: description-content-type
 Dynamic: keywords
 Dynamic: license-file
 Dynamic: requires-dist
-Dynamic: summary
 
 # EGA - RefgenDetector
 

{refgendetector-3.0.0 → refgendetector-3.0.2}/src/RefgenDetector.egg-info/SOURCES.txt

@@ -13,4 +13,6 @@ src/refgenDetector/chromosomes_dict.py
 src/refgenDetector/ref_manager.py
 src/refgenDetector/reference_genome_dictionaries.py
 src/refgenDetector/refgenDetector_main.py
-src/refgenDetector/variant_files.py
+src/refgenDetector/variant_files.py
+src/refgenDetector/exceptions/NoFileException.py
+src/refgenDetector/exceptions/__init__.py

{refgendetector-3.0.0 → refgendetector-3.0.2}/src/RefgenDetector.egg-info/requires.txt

@@ -1,7 +1,7 @@
-argparse
 pysam
 psutil
 rich
 pandas
 dnspython
 msgpack
+numpy

{refgendetector-3.0.0 → refgendetector-3.0.2}/src/refgenDetector/aligment_files.py

@@ -1,11 +1,5 @@
 import os
 import sys
-# Add the parent directory to the Python path
-current_dir = os.path.dirname(os.path.abspath(__file__))
-parent_dir = os.path.dirname(current_dir)
-sys.path.insert(0, parent_dir)
-from refgenDetector.reference_genome_dictionaries import *
-from refgenDetector.exceptions.NoFileException import *
 import argparse
 import csv
 import gzip
@@ -14,6 +8,15 @@ import psutil
 import time
 from rich.console import Console
 
+try:
+    # Works when installed as a pip package
+    from .reference_genome_dictionaries import *
+    from .exceptions.NoFileException import *
+except ImportError:
+    # Works when run directly as a script
+    from refgenDetector.reference_genome_dictionaries import *
+    from refgenDetector.exceptions.NoFileException import *
+
 console = Console()
 
 def intersection_targetfile_referencerepo(dict_SN_LN, reference_genome):

refgendetector-3.0.2/src/refgenDetector/exceptions/NoFileException.py

@@ -0,0 +1,4 @@
+class NoFileException(Exception):
+    def __init__(self):
+        self.message = "File Does Not Exist"
+        super().__init__(self.message)

{refgendetector-3.0.0 → refgendetector-3.0.2}/src/refgenDetector/ref_manager.py

@@ -1,7 +1,13 @@
 import sys
 import json
 from pathlib import Path
-from reference_genome_dictionaries import major_releases
+try:
+    # Works when installed as a pip package
+    from .reference_genome_dictionaries import *
+except ImportError:
+    # Works when run directly as a script
+    from reference_genome_dictionaries import *
+
 
 DEFAULT_MAJOR_RELEASES = dict(major_releases)
 

{refgendetector-3.0.0 → refgendetector-3.0.2}/src/refgenDetector/refgenDetector_main.py

@@ -3,12 +3,12 @@
 """ refgenDetector.py: Script to infer the reference genome used to create a BAM or CRAM"""
 
 __author__ = "Mireia Marin Ginestar"
-__version__ = "2.0"
+__version__ = "3.0.1"
 __maintainer__ = "Mireia Marin Ginestar"
 __email__ = "mireia.marin@crg.eu"
 __status__ = "Developement"
 
-version = "2.0.0"
+version = "3.0.1"
 
 import os
 import sys
@@ -18,16 +18,18 @@ import pysam
 import psutil
 import time
 from rich.console import Console
-
-# Add the parent directory to the Python path
-current_dir = os.path.dirname(os.path.abspath(__file__))
-parent_dir = os.path.dirname(current_dir)
-sys.path.insert(0, parent_dir)
-
-from reference_genome_dictionaries import *
-from exceptions.NoFileException import *
-from aligment_files import *
-from variant_files import *
+try:
+    # Works when installed as a pip package
+    from .reference_genome_dictionaries import *
+    from .exceptions.NoFileException import *
+    from .aligment_files import *
+    from .variant_files import *
+except ImportError:
+    # Works when run directly as a script
+    from reference_genome_dictionaries import *
+    from exceptions.NoFileException import *
+    from aligment_files import *
+    from variant_files import *
 
 console = Console()
 

{refgendetector-3.0.0 → refgendetector-3.0.2}/src/refgenDetector/variant_files.py

@@ -3,14 +3,20 @@ import sys
 import time
 import pandas as pd
 from dns.inet import inet_pton
-from aligment_files import comparison
-from chromosomes_dict import *
 from rich.console import Console
-import json
 import os
 import numpy as np 
 import msgpack
-import pysam 
+try:
+    # Works when installed as a pip package
+    from .aligment_files import *
+    from .chromosomes_dict import *
+except ImportError:
+    # Works when run directly as a script
+    from aligment_files import comparison
+    from chromosomes_dict import *
+
+
 
 final_results = []
 console = Console(highlight=False)