Merge pull request #50 from AlexandrovLab/development

Development
AlexandrovLab · Aug 5, 2024 · db6d54c · db6d54c
2 parents dbe0f27 + 1e541a4
commit db6d54c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,17 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [1.3.24] - 2024-08-01
+
+### Added
+- Added environmental variable `SIGPROFILERPLOTTING_VOLUME` to enhance configurability.
+
+### Fixed
+- Ensured correct file path construction with `os.path.join()`.
+- Updated CLI to handle boolean arguments using `str2bool`, resolving an issue where boolean strings like `False` were incorrectly evaluated as `True`.
+- Stopped unecessary output directory creation when the output format is PIL_Image.
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/2aj6t/wiki/home/) [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause) [![Build Status](https://travis-ci.com/AlexandrovLab/SigProfilerPlotting.svg?branch=master)](https://app.travis-ci.com/AlexandrovLab/SigProfilerPlotting)
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/2aj6t/wiki/home/) [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause) [![Build Status](https://app.travis-ci.com/AlexandrovLab/SigProfilerPlotting.svg?branch=master)](https://app.travis-ci.com/AlexandrovLab/SigProfilerPlotting)
 
 # SigProfilerPlotting
 SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

diff --git a/setup.py b/setup.py
@@ -14,7 +14,7 @@ def readme():
         return f.read()
 
 
-VERSION = "1.3.23"
+VERSION = "1.3.24"
 
 
 def write_version_py(filename="sigProfilerPlotting/version.py"):
@@ -23,7 +23,7 @@ def write_version_py(filename="sigProfilerPlotting/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-update = 'Upgrade v1.3.23: Update SBS4608 custom_text_upper, custom_text_lower, custom_text_middle.'
+update = 'Upgrade v1.3.24: Make output path handling more robust with os.path.join() and add environmental variable SIGPROFILERPLOTTING_VOLUME'
     
     """
     fh = open(filename, "w")

diff --git a/sigProfilerPlotting/controllers/cli_controller.py b/sigProfilerPlotting/controllers/cli_controller.py
@@ -3,6 +3,17 @@
 import sigProfilerPlotting as sigPlt
 
 
+def str2bool(v):
+    if isinstance(v, bool):
+        return v
+    if v.lower() in ("yes", "true", "t", "y", "1"):
+        return True
+    elif v.lower() in ("no", "false", "f", "n", "0"):
+        return False
+    else:
+        raise argparse.ArgumentTypeError("Boolean value expected.")
+
+
 # Common parser setup for shared arguments
 def common_plotting_arguments(parser):
     parser.add_argument("matrix_path", help="The path to the input matrix file.")
@@ -12,7 +23,12 @@ def common_plotting_arguments(parser):
     parser.add_argument("project", help="The name of the project.")
     parser.add_argument("plot_type", help="The type of plot to generate.")
     parser.add_argument(
-        "--percentage", action="store_true", help="Display percentages in the plot."
+        "--percentage",
+        type=str2bool,
+        nargs="?",
+        const=True,
+        default=False,
+        help="Display percentages in the plot.",
     )
     parser.add_argument(
         "--custom_text_upper", help="Custom text to display at the top of the plot."
@@ -40,7 +56,7 @@ def common_plotting_arguments(parser):
 
 def parse_arguments_sbs(args: List[str]) -> argparse.Namespace:
     parser = argparse.ArgumentParser(
-        prog="SigProfilerPlotting plotDBS", description="Generate DBS plots."
+        prog="SigProfilerPlotting plotSBS", description="Generate SBS plots."
     )
     common_plotting_arguments(parser)
     return parser.parse_args(args)
@@ -72,10 +88,20 @@ def parse_arguments_sv(args: List[str]) -> argparse.Namespace:
     )
     parser.add_argument("project", help="The name of the project.")
     parser.add_argument(
-        "--percentage", action="store_true", help="Display percentages in the plot."
+        "--percentage",
+        type=str2bool,
+        nargs="?",
+        const=True,
+        default=False,
+        help="Display percentages in the plot.",
     )
     parser.add_argument(
-        "--aggregate", action="store_true", help="Aggregate all samples."
+        "--aggregate",
+        type=str2bool,
+        nargs="?",
+        const=True,
+        default=False,
+        help="Aggregate all samples.",
     )
     parser.add_argument(
         "--savefig_format",
@@ -102,14 +128,26 @@ def parse_arguments_cnv(args: List[str]) -> argparse.Namespace:
     )
     parser.add_argument("project", help="The name of the project.")
     parser.add_argument(
-        "--percentage", action="store_true", help="Display percentages in the plot."
+        "--percentage",
+        type=str2bool,
+        nargs="?",
+        const=True,
+        default=False,
+        help="Display percentages in the plot.",
     )
     parser.add_argument(
-        "--aggregate", action="store_true", help="Aggregate data for the plot."
+        "--aggregate",
+        type=str2bool,
+        nargs="?",
+        const=True,
+        default=False,
+        help="Aggregate data for the plot.",
     )
     parser.add_argument(
         "--read_from_file",
-        action="store_true",
+        type=str2bool,
+        nargs="?",
+        const=True,
         default=True,
         help="Read data from a file for the plot.",
     )

diff --git a/sigProfilerPlotting/sigProfilerPlotting.py b/sigProfilerPlotting/sigProfilerPlotting.py
@@ -105,7 +105,8 @@ def clear_plotting_memory():
 # the figures are saved to a dictionary of buffers
 def output_results(savefig_format, output_path, project, figs, context_type, dpi=100):
     if savefig_format.lower() == "pdf":
-        pp = PdfPages(output_path + context_type + "_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"{context_type}_plots_{project}.pdf")
+        pp = PdfPages(file_path)
         for fig in figs:
             if context_type in ("CNV_48", "SV_32"):
                 figs[fig].savefig(pp, format="pdf", bbox_inches="tight")
@@ -241,6 +242,12 @@ def get_default_96labels():
 
 
 def make_pickle_file(context="SBS96", return_plot_template=False, volume=None):
+
+    # The environmental variable takes precedence over the volume argument
+    # If the environmental variable is not set, the volume argument is used
+    volume = os.getenv("SIGPROFILERPLOTTING_VOLUME", volume)
+
+    # Use the default volume when no environmental variable or volume argument is provided
     if volume is None:
         volume = SPP_TEMPLATES
 
@@ -743,7 +750,6 @@ def make_pickle_file(context="SBS96", return_plot_template=False, volume=None):
         else:
             pickle.dump(plot1, open(path, "wb"))
             return plot1
-
     elif context == "DBS78":
         plot_custom_text = False
         pcawg = False
@@ -1016,7 +1022,6 @@ def make_pickle_file(context="SBS96", return_plot_template=False, volume=None):
         else:
             pickle.dump(plot1, open(path, "wb"))
             return plot1
-
     elif context == "ID83":
         plt.rcParams["axes.linewidth"] = 2
         plot1 = plt.figure(figsize=(43.93, 12))
@@ -2090,7 +2095,7 @@ def plot(counts, labels, sample, project, percentage, aggregate=False):
         return fig
 
     # create the output directory if it doesn't exist
-    if not os.path.exists(output_path):
+    if not os.path.exists(output_path) and savefig_format.lower() != "pil_image":
         os.makedirs(output_path)
 
     # To reindex the input data
@@ -2625,7 +2630,7 @@ def plot(counts, labels, sample, project, percentage, aggregate=False):
         return fig
 
     # create the output directory if it doesn't exist
-    if not os.path.exists(output_path):
+    if not os.path.exists(output_path) and savefig_format.lower() != "pil_image":
         os.makedirs(output_path)
 
     df = pd.DataFrame()
@@ -2710,7 +2715,7 @@ def plotSBS(
     load_custom_fonts()
 
     # create the output directory if it doesn't exist
-    if not os.path.exists(output_path):
+    if not os.path.exists(output_path) and savefig_format.lower() != "pil_image":
         os.makedirs(output_path)
 
     if plot_type == "96":
@@ -3021,7 +3026,8 @@ def plotSBS(
                 sys.exit(
                     "The matrix does not match the correct SBS192 format. Please check you formatting and rerun this plotting function."
                 )
-        pp = PdfPages(output_path + "SBS_384_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"SBS_384_plots_{project}.pdf")
+        pp = PdfPages(file_path)
         mutations = OrderedDict()
         try:
             with open(matrix_path) as f:
@@ -3537,7 +3543,8 @@ def plotSBS(
                     "The matrix does not match the correct SBS288 format. Please check you formatting and rerun this plotting function."
                 )
 
-        pp = PdfPages(output_path + "SBS_384_extended_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"SBS_384_extended_plots_{project}.pdf")
+        pp = PdfPages(file_path)
         mutations = OrderedDict()
         try:
             with open(matrix_path) as f:
@@ -4087,8 +4094,8 @@ def plotSBS(
                 sys.exit(
                     "The matrix does not match the correct SBS6 format. Please check you formatting and rerun this plotting function."
                 )
-
-        pp = PdfPages(output_path + "SBS_6_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"SBS_6_plots_{project}.pdf")
+        pp = PdfPages(file_path)
 
         mutations = OrderedDict()
         total_count = []
@@ -4322,8 +4329,8 @@ def plotSBS(
                 sys.exit(
                     "The matrix does not match the correct SBS192 format. Please check you formatting and rerun this plotting function."
                 )
-
-        pp = PdfPages(output_path + "SBS_24_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"SBS_24_plots_{project}.pdf")
+        pp = PdfPages(file_path)
         mutations = OrderedDict()
 
         try:
@@ -4580,7 +4587,8 @@ def plotSBS(
                     "The matrix does not match the correct SBS1536 format. Please check you formatting and rerun this plotting function."
                 )
 
-        pp = PdfPages(output_path + "SBS_1536_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"SBS_1536_plots_{project}.pdf")
+        pp = PdfPages(file_path)
 
         mutations_96 = OrderedDict()
         path_list = matrix_path.split("/")
@@ -5911,7 +5919,8 @@ def plotSBS(
                     "The matrix does not match the correct SBS4608 format. Please check you formatting and rerun this plotting function."
                 )
 
-        pp = PdfPages(output_path + "SBS_4608_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"SBS_4608_plots_{project}.pdf")
+        pp = PdfPages(file_path)
 
         path_list = matrix_path.split("/")
         extension = path_list[-1].split(".")
@@ -7033,7 +7042,7 @@ def plotSBS(
 
                 fontsize_custom = 25
                 fontweight_custom = "bold"
-                fontcolor_custom = ("black")
+                fontcolor_custom = "black"
                 fontname_custom = "Arial"
                 ha_custom = "left"
 
@@ -7751,7 +7760,8 @@ def plotSBS(
                     "The matrix does not match the correct SBS288 format. Please check you formatting and rerun this plotting function."
                 )
 
-        pp = PdfPages(output_path + "SBS_288_Normalized_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"SBS_288_Normalized_plots_{project}.pdf")
+        pp = PdfPages(file_path)
 
         mutations = OrderedDict()
         mutations_TSB = OrderedDict()
@@ -8315,9 +8325,9 @@ def plotSBS(
 
     else:
         print(
-            "The provided plot_type:",
+            "Error: The function plotSBS does not support plot_type",
             plot_type,
-            "is not supported by this plotting function",
+            "so no plot has been generated."
         )
 
 
@@ -8335,7 +8345,7 @@ def plotID(
     dpi=100,
 ):
     # create the output directory if it doesn't exist
-    if not os.path.exists(output_path):
+    if not os.path.exists(output_path) and savefig_format.lower() != "pil_image":
         os.makedirs(output_path)
 
     # load custom fonts for plotting
@@ -8676,7 +8686,8 @@ def plotID(
                 sys.exit(
                     "The matrix does not match the correct SBS96 format. Please check you formatting and rerun this plotting function."
                 )
-        pp = PdfPages(output_path + "ID_simple_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"ID_simple_plots_{project}.pdf")
+        pp = PdfPages(file_path)
 
         indel_types = [
             "1:Del:C:1",
@@ -9211,10 +9222,7 @@ def plotID(
                 os.remove(pdf_path)
 
     elif (
-        plot_type == "96"
-        or plot_type == "ID96"
-        or plot_type == "96ID"
-        or plot_type == "IDSB"
+        plot_type == "IDSB"
         or plot_type == "415"
     ):
         with open(matrix_path) as f:
@@ -9229,7 +9237,8 @@ def plotID(
                     "The matrix does not match the correct ID-96 format. Please check you formatting and rerun this plotting function."
                 )
 
-        pp = PdfPages(output_path + "ID_TSB_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"ID_TSB_plots_{project}.pdf")
+        pp = PdfPages(file_path)
 
         indel_types_tsb = []
         tsb_I = ["T", "U", "N", "B", "Q"]
@@ -10294,9 +10303,9 @@ def plotID(
 
     else:
         print(
-            "The provided plot_type:",
+            "Error: The function plotID does not support plot_type",
             plot_type,
-            "is not supported by this plotting function",
+            "so no plot has been generated."
         )
 
 
@@ -10314,7 +10323,7 @@ def plotDBS(
     dpi=100,
 ):
     # create the output directory if it doesn't exist
-    if not os.path.exists(output_path):
+    if not os.path.exists(output_path) and savefig_format.lower() != "pil_image":
         os.makedirs(output_path)
 
     # load custom fonts for plotting
@@ -10736,7 +10745,8 @@ def plotDBS(
                     "The matrix does not match the correct SBS96 format. Please check you formatting and rerun this plotting function."
                 )
 
-        pp = PdfPages(output_path + "DBS_186_plots_" + project + ".pdf")
+        file_path = os.path.join(output_path, f"DBS_186_plots_{project}.pdf")
+        pp = PdfPages(file_path)
 
         dinucs = [
             "TT>GG",
@@ -11222,7 +11232,7 @@ def plotDBS(
 
     else:
         print(
-            "The provided plot_type:",
+            "Error: The function plotDBS does not support plot_type",
             plot_type,
-            "is not supported by this plotting function",
+            "so no plot has been generated."
         )
diff --git a/sigProfilerPlotting/version.py b/sigProfilerPlotting/version.py
@@ -1,7 +1,7 @@
 
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
-short_version = '1.3.22'
-version = '1.3.22'
-update = 'Upgrade v1.3.22: Update input_processing index.name handling to be more robust.'
+short_version = '1.3.24'
+version = '1.3.24'
+update = 'Upgrade v1.3.24: Make output path handling more robust with os.path.join() and add environmental variable SIGPROFILERPLOTTING_VOLUME'