-V, --version flag added to all argparse commands

Author: vineetbansal

custom/GATK4-CNV/gatk4cnsToBB.py

@@ -6,6 +6,7 @@
 import numpy as np
 
 from collections import deque
+from hatchet import __version__
 
 
 def parse_args():
@@ -17,6 +18,7 @@ def parse_args():
     parser.add_argument("-r", "--devRDR", type=float, required=False, default=0.05, help='Standard deviation for the RDR of bins obtained from RDR of the corresponding segment (default: 0,05).')
     parser.add_argument("-a", "--devBAF", type=float, required=False, default=0.02, help='Standard deviation for the RDR of bins obtained from RDR of the corresponding segment (default: 0.02).')
     parser.add_argument("-s", "--seed", type=int, required=False, default=None, help='Starting seed for random number generator (default: not specified).')
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args()
 
     samples = args.INPUT.strip().split()

setup.py

@@ -76,7 +76,7 @@ def build_extension(self, ext):
 
 setup(
     name='hatchet',
-    version='0.3.0',
+    version='0.3.1',
     packages=['hatchet', 'hatchet.utils', 'hatchet.bin'],
     package_dir={'': 'src'},
     package_data={'hatchet': ['hatchet.ini']},

src/hatchet/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.3.0'
+__version__ = '0.3.1'
 
 import os.path
 from importlib.resources import path
@@ -10,7 +10,7 @@
     filenames = [ini_file]
     # If a hatchet.ini file exists where we were imported from, use it after the pre-packaged .ini file
     # This allows overriding of values without having to alter the pre-packaged .ini file, which may
-    # be buried deep inside the site-packages folder.s
+    # be buried deep inside the site-packages folder.
     if os.path.exists('hatchet.ini'):
         filenames.append('hatchet.ini')
     config = Config('hatchet', filenames)

src/hatchet/bin/HATCHet-preprocess.py

@@ -1,20 +1,13 @@
 #!/usr/bin/env python3
-
-
-
-import sys, os
+import os
 import argparse
 import subprocess as sp
 import multiprocessing as mp
 import shlex
 import re
 
-utils = os.path.join(os.path.dirname(os.path.abspath(__file__)), os.pardir, 'utils')
-if not os.path.isdir(utils):
-    raise ValueError("utils directory not found in HATCHet's home directory i.e. {}, is anything been moved?".format(utils))
-sys.path.append(utils)
-from Supporting import *
-from hatchet import config
+from hatchet.utils.Supporting import *
+from hatchet import config, __version__
 
 
 def parse_args():
@@ -33,6 +26,7 @@ def parse_args():
     parser.add_argument("--samtools", required=False, default=config.paths.samtools, type=str, help="Path to the directory to \"samtools\" executable, required in default mode (default: samtools is directly called as it is in user $PATH)")
     parser.add_argument("--seed", required=False, type=int, default=config.preprocess.seed, help="Random seed for replication (default: None)")
     parser.add_argument("-j","--jobs", required=False, type=int, default=config.preprocess.jobs, help="Number of parallele jobs to use (default: equal to number of available processors)")
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args()
 
     tumor = set(t for t in args.tumor.split())

src/hatchet/bin/HATCHet.py

@@ -9,7 +9,7 @@
 import shlex
 from collections import Counter
 
-from hatchet import config
+from hatchet import config, __version__
 
 
 def parsing_arguments(args=None):
@@ -49,6 +49,7 @@ def parsing_arguments(args=None):
     parser.add_argument("--diploid", action='store_true', default=config.compute_cn.diploid, required=False, help="Force the tumor clones to be diploid without WGD (default: false)")
     parser.add_argument("--tetraploid", action='store_true', default=config.compute_cn.tetraploid, required=False, help="Force the tumor clones to be tetraploid with an occured WGD (default: false)")
     parser.add_argument("-v","--verbosity", type=int, required=False, default=config.compute_cn.verbosity, help="Level of verbosity among: none (0), essential (1), verbose (2), and debug (3) (default: 1)")
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     if not os.path.isfile(args.SOLVER):

src/hatchet/utils/ArgParsing.py

@@ -4,7 +4,7 @@
 import subprocess
 
 from . import Supporting as sp
-from hatchet import config
+from hatchet import config, __version__
 
 
 def parse_genotype_snps_arguments(args=None):
@@ -27,6 +27,7 @@ def parse_genotype_snps_arguments(args=None):
     parser.add_argument("-E","--newbaq", required=False, action='store_true', default=config.genotype_snps.newbaq, help="Recompute alignment of reads on the fly during SNP calling (default: false)")
     parser.add_argument("-o", "--outputsnps", required=False, default=config.genotype_snps.outputsnps, type=str, help="Output folder for SNPs separated by chromosome (default: ./)")
     parser.add_argument("-v", "--verbose", action='store_true', default=config.genotype_snps.verbose, required=False, help="Use verbose log messages")
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     # Parse BAM files, check their existence, and infer or parse the corresponding sample names
@@ -110,6 +111,7 @@ def parse_count_alleles_arguments(args=None):
     parser.add_argument("-o", "--outputtumors", required=False, default=config.count_alleles.outputtumors, type=str, help="Output filename for allele counts in tumor samples (default: standard output)")
     parser.add_argument("-l", "--outputsnps", required=False, default=config.count_alleles.outputsnps, type=str, help="Output directory for lists of selected SNPs (default: ./)")
     parser.add_argument("-v", "--verbose", action='store_true', default=config.count_alleles.verbose, required=False, help="Use verbose log messages")
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     # Parse BAM files, check their existence, and infer or parse the corresponding sample names
@@ -218,6 +220,7 @@ def parse_count_reads_arguments(args=None):
     parser.add_argument("-o", "--outputtumors", required=False, default=config.count_reads.outputtumors, type=str, help="Output filename for allele counts in tumor samples (default: standard output)")
     parser.add_argument("-t", "--outputtotal", required=False, default=config.count_reads.outputtotal, type=str, help="Output filename for total read counts in all tumor samples (default: \"total_read.counts\")")
     parser.add_argument("-v", "--verbose", action='store_true', default=config.count_reads.verbose, required=False, help="Use verbose log messages")
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     # Parse BAM files, check their existence, and infer or parse the corresponding sample names
@@ -310,6 +313,7 @@ def parse_combine_counts_args(args=None):
     parser.add_argument("-e","--seed", type=int, required=False, default=config.combine_counts.seed, help='Random seed used for the normal distributions used in the clouds (default: 0)')
     parser.add_argument("-v", "--verbose", action='store_true', default=config.combine_counts.verbose, required=False, help="Use verbose log messages")
     parser.add_argument("-r", "--disablebar", action='store_true', default=config.combine_counts.disablebar, required=False, help="Disable progress bar")
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     if not os.path.isfile(args.normalbins):
@@ -377,6 +381,7 @@ def parse_cluster_bins_args(args=None):
     parser.add_argument("-R","--restarts", type=int, required=False, default=config.cluster_bins.restarts, help="Number of restarts performed by the clustering to choose the best (default: 10)")
     parser.add_argument("-v","--verbose", action='store_true', default=config.cluster_bins.verbose, required=False, help="Use verbose log messages")
     parser.add_argument("--disablebar", action='store_true', default=config.cluster_bins.disablebar, required=False, help="Disable progress bar")
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     if not os.path.isfile(args.BBFILE):
@@ -444,6 +449,7 @@ def parse_plot_bins_args(args=None):
     parser.add_argument("-x","--rundir", required=False, default=config.plot_bins.rundir, type=str, help='Running dirrectory where output the results (default: current directory)')
     parser.add_argument("--pdf", action='store_true', default=config.plot_bins.pdf, required=False, help="Output the bb_clustered figure in PDF format (default: PNG)")
     parser.add_argument("--dpi", required=False, default=config.plot_bins.dpi, type=int, help='DPI of PNG images (default: 900)')
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     if not os.path.isfile(args.INPUT):

src/hatchet/utils/plot_cn.py

@@ -25,7 +25,7 @@
 import itertools
 from itertools import cycle
 
-from hatchet import config
+from hatchet import config, __version__
 
 plt.style.use('ggplot')
 sns.set_style("whitegrid")
@@ -61,6 +61,7 @@ def parsing_arguments(args=None):
     parser.add_argument("--ymin", required=False, default=config.plot_cn.ymin, type=int, help='Minimum values in y-axis (default: automatically inferred)"')
     parser.add_argument("--clonepalette", required=False, default=config.plot_cn.clonepalette, type=str, help='Palette for coloring the clones among Set1, Set2, Set3, Paired (default: Set1)"')
     parser.add_argument("--linkage", required=False, default=config.plot_cn.linkage, type=str, help='Linkage method used for clustering (default: single, available \{single, complete, average, weighted, centroid, median, ward\} from SciPy)"')
+    parser.add_argument("-V", "--version", action='version', version=f'%(prog)s {__version__}')
     args = parser.parse_args(args)
 
     if len(args.INPUT.split()) == 0: