add version information

Author: ATPs

setup.py

@@ -1,9 +1,16 @@
 from setuptools import setup, find_packages
 import os
 folder = os.path.dirname(os.path.abspath(__file__))
+
+# Read version from version file
+def get_version():
+    version_file = os.path.join(folder, 'src', 'version')
+    with open(version_file, 'r') as f:
+        return f.read().strip()
+
 setup(
     name="precisionprodb",  # Your package name
-    version="2.0.2",  # Package version
+    version=get_version(),  # Package version read from src/version file
     # packages=['.',],  # Automatically find sub-packages under `src`
     package_dir={'': 'src'},
     install_requires=[  # Your dependencies

src/PrecisionProDB.py

@@ -7,6 +7,15 @@
 import re
 import buildSqlite
 
+def get_version():
+    """Read version from version file"""
+    try:
+        version_file = os.path.join(os.path.dirname(__file__), 'version')
+        with open(version_file, 'r') as f:
+            return f.read().strip()
+    except FileNotFoundError:
+        return "unknown"
+
 description = '''
 PrecisionProDB, a personal proteogenomic tool which outputs a new reference protein based on the variants data. 
 A VCF or /a tsv file can be used as the variant input. If the variant file is in tsv format, at least four columns are required in the header: chr, pos, ref, alt. Additional columns will be ignored. Try to Convert the file to proper format if you have a bed file or other types of variant file. The pos column is 1-based like in the vcf file.
@@ -15,6 +24,7 @@
 def main():
     import argparse
     parser = argparse.ArgumentParser(description=description)
+    parser.add_argument('-v', '--version', action='version', version=f'PrecisionProDB {get_version()}')
     parser.add_argument('-g','--genome', help = 'the reference genome sequence in fasta format. It can be a gzip file', default='')
     parser.add_argument('-f', '--gtf', help='gtf file with CDS and exon annotations. It can be a gzip file', default='')
     parser.add_argument('-m', '--mutations', help='''

src/version

@@ -0,0 +1 @@
+2.3.0