ModDotPlot 0.9.0__tar.gz → 0.9.1__tar.gz

moddotplot-0.9.1/PKG-INFO

@@ -0,0 +1,48 @@
+Metadata-Version: 2.2
+Name: ModDotPlot
+Version: 0.9.1
+Author: Michael Schatz, Adam Phillippy
+Author-email: Alex Sweeten <alex.sweeten@nih.gov>
+Maintainer-email: Alex Sweeten <alex.sweeten@nih.gov>
+License: MIT License
+        
+        Copyright (c) 2024 MarBL
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Keywords: dotplot,sketching,modimizer,heatmap
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pysam
+Requires-Dist: pandas
+Requires-Dist: plotly
+Requires-Dist: dash
+Requires-Dist: plotnine==0.12.4
+Requires-Dist: palettable
+Requires-Dist: mmh3
+Requires-Dist: tk
+Requires-Dist: setproctitle
+Requires-Dist: numpy
+Requires-Dist: pillow
+Requires-Dist: patchworklib==0.6.3
+Requires-Dist: cairosvg
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"

{moddotplot-0.9.0 → moddotplot-0.9.1}/README.md

@@ -19,7 +19,7 @@
 
 ## Cite
 
-Alexander P Sweeten, Michael C Schatz, Adam M Phillippy, ModDotPlot—rapid and interactive visualization of tandem repeats, Bioinformatics, Volume 40, Issue 8, August 2024, btae493, https://doi.org/10.1093/bioinformatics/btae493
+Alexander P Sweeten, Michael C Schatz, Adam M Phillippy, ModDotPlot—rapid and interactive visualization of tandem repeats, Bioinformatics, Volume 40, Issue 8, August 2024, btae493, [https://doi.org/10.1093/bioinformatics/btae493](https://pmc.ncbi.nlm.nih.gov/articles/PMC11321072/)
 
 If you use ModDotPlot for your research, please cite our software!
 
@@ -386,10 +386,10 @@ For bug reports or general usage questions, please raise a GitHub issue, or emai
 
 ## Known Issues
 
-- Plot width and xlim (limiting the x axis to a different amount) currently do not work. I plan to have those working in v0.9.0.
+- 
 
 - Mac users might encounter the following unexpected command line output: `/bin/sh: lscpu: command not found`. This is a known issue with Plotnine, the Python plotting library used by ModDotPlot. This can be safely ignored.
 
-- If you encounter an error with the following traceback: `rv = reductor(4) TypeError: cannot pickle 'generator' object`, ths means that you have a newer version of Plotnine that is incompatible with ModDotPlot. Please uninstall plotnine and reinstall version 0.12.4 `pip install plotnine==0.12.4`. 
+- If you encounter an error with the following traceback: `rv = reductor(4) TypeError: cannot pickle 'generator' object`, this means that you have a newer version of Plotnine that is incompatible with ModDotPlot. Please uninstall plotnine and reinstall version 0.12.4 `pip install plotnine==0.12.4`. 
 
-- In interactive mode, comparing sequences of two sizes will lead to errors in zooming for the larger sequence. I plan to fix this in v0.9.0.
+- There are a number of errors 

{moddotplot-0.9.0 → moddotplot-0.9.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ModDotPlot"
-version = "0.9.0"
+version = "0.9.1"
 requires-python = ">= 3.7"
 dependencies = [
   "pysam",
@@ -18,7 +18,8 @@ dependencies = [
   "setproctitle",
   "numpy",
   "pillow",
-  "patchworklib"
+  "patchworklib==0.6.3",
+  "cairosvg"
 ]
 authors = [
   {name = "Alex Sweeten", email = "alex.sweeten@nih.gov"},
@@ -28,7 +29,8 @@ authors = [
 maintainers = [
   {name = "Alex Sweeten", email = "alex.sweeten@nih.gov"}
 ]
-readme = {file = "README.md", content-type = "text/markdown"}
+readme = {file = "README.txt", content-type = "text/markdown"}
+license = {file = "LICENSE"}
 keywords = ["dotplot", "sketching", "modimizer", "heatmap"]
 
 [project.scripts]
@@ -40,12 +42,3 @@ test = [
     "pytest",
     "pytest-cov"
 ]
-
-[tool.hatch.build.targets.sdist]
-exclude = [
-  "/.github",
-  "/docs",
-]
-
-[tool.hatch.build.targets.wheel]
-packages = ["src/moddotplot"]

moddotplot-0.9.1/src/ModDotPlot.egg-info/PKG-INFO

@@ -0,0 +1,48 @@
+Metadata-Version: 2.2
+Name: ModDotPlot
+Version: 0.9.1
+Author: Michael Schatz, Adam Phillippy
+Author-email: Alex Sweeten <alex.sweeten@nih.gov>
+Maintainer-email: Alex Sweeten <alex.sweeten@nih.gov>
+License: MIT License
+        
+        Copyright (c) 2024 MarBL
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Keywords: dotplot,sketching,modimizer,heatmap
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pysam
+Requires-Dist: pandas
+Requires-Dist: plotly
+Requires-Dist: dash
+Requires-Dist: plotnine==0.12.4
+Requires-Dist: palettable
+Requires-Dist: mmh3
+Requires-Dist: tk
+Requires-Dist: setproctitle
+Requires-Dist: numpy
+Requires-Dist: pillow
+Requires-Dist: patchworklib==0.6.3
+Requires-Dist: cairosvg
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"

{moddotplot-0.9.0 → moddotplot-0.9.1}/src/ModDotPlot.egg-info/requires.txt

@@ -9,7 +9,8 @@ tk
 setproctitle
 numpy
 pillow
-patchworklib
+patchworklib==0.6.3
+cairosvg
 
 [test]
 pytest

{moddotplot-0.9.0 → moddotplot-0.9.1}/src/moddotplot/const.py

@@ -1,4 +1,4 @@
-VERSION = "0.9.0"
+VERSION = "0.9.1"
 COLS = [
     "#query_name",
     "query_start",

{moddotplot-0.9.0 → moddotplot-0.9.1}/src/moddotplot/moddotplot.py

@@ -179,7 +179,7 @@ def get_parser():
         "-b",
         "--bed",
         default=argparse.SUPPRESS,
-        help="Path to input bed file(s). Exclusively used in static mode.",
+        help="Path to input paired-end bed file(s). Exclusively used in static mode.",
         nargs="+",
     )
 
@@ -273,7 +273,7 @@ def get_parser():
     )
 
     static_parser.add_argument(
-        "--width", default=9, type=float, nargs="+", help="Plot width."
+        "--width", default=18, type=float, help="Plot width (also height for _FULL)."
     )
 
     static_parser.add_argument("--dpi", default=600, type=int, help="Plot dpi.")
@@ -321,8 +321,15 @@ def get_parser():
         "--axes-ticks",
         default=None,
         nargs="+",
+        type=int,
         help="Tick labels to include in x and y axis for custom plots.",
     )
+    # CURRENTLY NOT WORKING
+    static_parser.add_argument(
+        "--axes-number",
+        default=7,
+        help="Number of axis ticks labels to include in x and y axis for custom plots, including 0 and seq_length. A minimum of 2 is required, maximum 25.",
+    )
 
     static_parser.add_argument(
         "--bin-freq",
@@ -345,10 +352,21 @@ def get_parser():
     static_parser.add_argument(
         "--grid-only",
         action="store_true",
-        help="Plot comparative plots in an NxN grid like format, skipping individual plots",
+        help="Plot comparative plots in an NxN grid like format, skipping individual plots.",
+    )
+
+    static_parser.add_argument(
+        "--vector",
+        choices=["svg", "pdf", "ps"],
+        default="svg",
+        help="Output format for vector format.",
     )
 
-    # TODO: Implement static mode logging options
+    static_parser.add_argument(
+        "--deraster",
+        action="store_true",
+        help="De-rasterize dotplot in vector format. Note this can lead to large image sizes and make it unusable in image editing software.",
+    )
 
     return parser
 
@@ -433,14 +451,13 @@ def main():
                 args.breakpoints = config.get("breakpoints", args.breakpoints)
                 args.bin_freq = config.get("bin_freq", args.bin_freq)
 
-            # TODO: Include logging options here
-        # Check if conflicitng command line args
-        if args.grid or args.grid_only:
+        #
+        """if args.grid or args.grid_only:
             if not (args.compare or args.compare_only) and not args.bed:
                 print(
                     f"Option --grid was selected, but no comparative plots will be produced. Please rerun ModDotPlot with the `--compare` or `--compare-only` option.\n"
                 )
-                sys.exit(10)
+                sys.exit(10)"""
 
         # -----------INPUT COMMAND VALIDATION-----------
         # TODO: More tests!
@@ -465,118 +482,140 @@ def main():
                 double_vals = []
                 single_val_name = []
                 double_val_name = []
-            try:
-                for bed in args.bed:
-                    # If args.bed is provided as input, run static mode directly from the bed file. Skip counting input k-mers.
-                    df = read_df_from_file(bed)
-
-                    unique_query_names = df["#query_name"].unique()
-                    unique_reference_names = df["reference_name"].unique()
-                    assert len(unique_query_names) == len(unique_reference_names)
-                    # TODO: Change this to allow for multiple seqs in bed file
-                    assert len(unique_reference_names) == 1
-                    self_id_scores = df[df["#query_name"] == df["reference_name"]]
-                    pairwise_id_scores = df[df["#query_name"] != df["reference_name"]]
+                xlim_val_grid = 0
+            for bed in args.bed:
+                # If args.bed is provided as input, run static mode directly from the bed file. Skip counting input k-mers.
+                df = read_df_from_file(bed)
+
+                unique_query_names = df["#query_name"].unique()
+                unique_reference_names = df["reference_name"].unique()
+                assert len(unique_query_names) == len(unique_reference_names)
+                assert len(unique_reference_names) == 1
+                self_id_scores = df[df["#query_name"] == df["reference_name"]]
+                pairwise_id_scores = df[df["#query_name"] != df["reference_name"]]
+                if not args.grid_only:
+                    print(f"Input bed file {bed} read successfully! Creating plots: \n")
+                # Create directory
+                if not args.output_dir:
+                    args.output_dir = os.getcwd()
+                if not os.path.exists(args.output_dir):
+                    os.makedirs(args.output_dir)
+                if len(self_id_scores) > 1:
                     if not args.grid_only:
-                        print(
-                            f"Input bed file {bed} read successfully! Creating plots... \n"
+                        create_plots(
+                            sdf=None,
+                            directory=args.output_dir if args.output_dir else ".",
+                            name_x=unique_query_names[0],
+                            name_y=unique_query_names[0],
+                            palette=args.palette,
+                            palette_orientation=args.palette_orientation,
+                            no_hist=args.no_hist,
+                            width=args.width,
+                            dpi=args.dpi,
+                            is_freq=args.bin_freq,
+                            xlim=args.axes_limits,
+                            custom_colors=args.colors,
+                            custom_breakpoints=args.breakpoints,
+                            from_file=df,
+                            is_pairwise=False,
+                            axes_labels=args.axes_ticks,
+                            axes_tick_number=args.axes_number,
+                            vector_format=args.vector,
+                            deraster=args.deraster,
                         )
-                    # Create directory
-                    if not args.output_dir:
-                        args.output_dir = os.getcwd()
-                    if not os.path.exists(args.output_dir):
-                        os.makedirs(args.output_dir)
-                    if len(self_id_scores) > 1:
-                        if not args.grid_only:
-                            create_plots(
-                                sdf=None,
-                                directory=args.output_dir if args.output_dir else ".",
-                                name_x=unique_query_names[0],
-                                name_y=unique_query_names[0],
-                                palette=args.palette,
-                                palette_orientation=args.palette_orientation,
-                                no_hist=args.no_hist,
-                                width=args.width,
-                                dpi=args.dpi,
-                                is_freq=args.bin_freq,
-                                xlim=args.axes_limits,
-                                custom_colors=args.colors,
-                                custom_breakpoints=args.breakpoints,
-                                from_file=df,
-                                is_pairwise=False,
-                                axes_labels=args.axes_ticks,
+                    if args.grid or args.grid_only:
+                        single_vals.append(df)
+                        single_val_name.append(unique_query_names[0])
+                        try:
+                            max_so_far = max(
+                                df["query_end"].max(), df["reference_end"].max()
                             )
-                        if args.grid or args.grid_only:
-                            single_vals.append(df)
-                            single_val_name.append(unique_query_names[0])
-                    # Case 2: Pairwise bed file
-                    if len(pairwise_id_scores) > 1:
-                        if not args.grid_only:
-                            create_plots(
-                                sdf=None,
-                                directory=args.output_dir if args.output_dir else ".",
-                                name_x=unique_query_names[0],
-                                name_y=unique_reference_names[0],
-                                palette=args.palette,
-                                palette_orientation=args.palette_orientation,
-                                no_hist=args.no_hist,
-                                width=args.width,
-                                dpi=args.dpi,
-                                is_freq=args.bin_freq,
-                                xlim=args.axes_limits,
-                                custom_colors=args.colors,
-                                custom_breakpoints=args.axes_ticks,
-                                from_file=df,
-                                is_pairwise=True,
-                                axes_labels=args.axes_ticks,
-                            )
-                        if args.grid or args.grid_only:
-                            double_vals.append(df)
-                            double_val_name.append(
-                                [unique_query_names[0], unique_reference_names[0]]
-                            )
-                # Exit once all bed files have been iterated through
-                if args.grid or args.grid_only:
-                    print(f"Creating a {len(sequences)}x{len(sequences)} grid.\n")
-                    create_grid(
-                        singles=single_vals,
-                        doubles=double_vals,
-                        directory=args.output_dir if args.output_dir else ".",
-                        palette=args.palette,
-                        palette_orientation=args.palette_orientation,
-                        no_hist=args.no_hist,
-                        single_names=single_val_name,
-                        double_names=double_val_name,
-                        is_freq=args.bin_freq,
-                        xlim=args.axes_limits,
-                        custom_colors=args.colors,
-                        custom_breakpoints=args.axes_ticks,
-                        axes_label=args.axes_ticks,
-                        is_bed=True,
-                    )
-                sys.exit(0)
-            except Exception as e:
-                # Exit code 7: Error getting info from bed file:
-                # TODO: Change to logs
-                print(f"Error in bed file: {e}")
-                sys.exit(7)
+                        except KeyError:
+                            max_so_far = max(df["q_en"].max(), df["r_en"].max())
+                        xlim_val_grid = (
+                            max_so_far if max_so_far > xlim_val_grid else xlim_val_grid
+                        )
+                # Case 2: Pairwise bed file
+                if len(pairwise_id_scores) > 1:
+                    if not args.grid_only:
+                        # Potentially sort
+                        create_plots(
+                            sdf=None,
+                            directory=args.output_dir if args.output_dir else ".",
+                            name_x=unique_query_names[0],
+                            name_y=unique_reference_names[0],
+                            palette=args.palette,
+                            palette_orientation=args.palette_orientation,
+                            no_hist=args.no_hist,
+                            width=args.width,
+                            dpi=args.dpi,
+                            is_freq=args.bin_freq,
+                            xlim=args.axes_limits,
+                            custom_colors=args.colors,
+                            custom_breakpoints=args.axes_ticks,
+                            from_file=df,
+                            is_pairwise=True,
+                            axes_labels=args.axes_ticks,
+                            axes_tick_number=args.axes_number,
+                            vector_format=args.vector,
+                            deraster=args.deraster,
+                        )
+                    if args.grid or args.grid_only:
+                        double_vals.append(df)
+                        double_val_name.append(
+                            [unique_query_names[0], unique_reference_names[0]]
+                        )
+            # Exit once all bed files have been iterated through
+            if args.grid or args.grid_only:
+                # Determine the number of sequences
+                if args.axes_limits:
+                    xlim_val_grid = args.axes_limits
+                print(
+                    f"Creating a {len(single_val_name)}x{len(single_val_name)} grid.\n"
+                )
+                create_grid(
+                    singles=single_vals,
+                    doubles=double_vals,
+                    directory=args.output_dir if args.output_dir else ".",
+                    palette=args.palette,
+                    palette_orientation=args.palette_orientation,
+                    single_names=single_val_name,
+                    double_names=double_val_name,
+                    is_freq=args.bin_freq,
+                    xlim=xlim_val_grid,
+                    custom_colors=args.colors,
+                    custom_breakpoints=args.axes_ticks,
+                    axes_label=args.axes_ticks,
+                    is_bed=True,
+                    width=args.width,
+                    breaks=args.axes_ticks,
+                    deraster=args.deraster,
+                    vector_format=args.vector,
+                )
+            sys.exit(0)
 
     # -----------INPUT SEQUENCE VALIDATION-----------
     seq_list = []
+    fasta_list = args.fasta.copy()
     for i in args.fasta:
-        isValidFasta(i)
-        headers = getInputHeaders(i)
-        if len(headers) > 1:
-            print(f"File {i} contains multiple fasta entries. \n")
-            counter = 1
-            for j in headers:
-                counter += 1
-        for j in headers:
-            seq_list.append(j)
+        try:
+            isValidFasta(i)
+            headers = getInputHeaders(i)
+
+            if len(headers) > 1:
+                print(f"File {i} contains multiple fasta entries.\n")
+
+            seq_list.extend(headers)  # Add all headers to seq_list
+
+        except Exception as e:
+            print(
+                f"\nUnable to open {i}. Please check it is correctly formatted or compressed...\n"
+            )
+            fasta_list.remove(i)
 
     # -----------LOAD SEQUENCES INTO MEMORY-----------
     kmer_list = []
-    for i in args.fasta:
+    for i in fasta_list:
         kmer_list.append(readKmersFromFile(i, args.kmer, False))
     k_list = [item for sublist in kmer_list for item in sublist]
     # Throw error if compare only selected with one sequence.
@@ -901,18 +940,6 @@ def main():
                 else:
                     seq_sparsity = 2 ** (int(math.log2(seq_sparsity - 1)) + 1)
                 expectation = round(win / seq_sparsity)
-                xaxis = 0
-                width = 0
-                """if isinstance(args.xaxis, int) or args.xaxis == None:
-                    xaxis = args.xaxis
-                else:
-                    assert len(args.xaxis) == len(sequences)
-                    xaxis = args.xaxis[i]"""
-                if isinstance(args.width, int):
-                    width = args.width
-                else:
-                    assert len(args.width) == len(sequences)
-                    width = args.width[i]
 
                 print(f"Computing self identity matrix for {sequences[i][0]}... \n")
                 # TODO: Logging here
@@ -952,7 +979,7 @@ def main():
                             bedfile.write("\t".join(map(str, row)) + "\n")
                     print(f"Saved bed file to {bedfile_output}\n")
 
-                if not args.no_plot:
+                if (not args.no_plot) and (not args.grid_only):
                     create_plots(
                         sdf=[bed],
                         directory=args.output_dir if args.output_dir else ".",
@@ -961,7 +988,7 @@ def main():
                         palette=args.palette,
                         palette_orientation=args.palette_orientation,
                         no_hist=args.no_hist,
-                        width=width,
+                        width=args.width,
                         dpi=args.dpi,
                         is_freq=args.bin_freq,
                         xlim=args.axes_limits,
@@ -970,16 +997,22 @@ def main():
                         from_file=None,
                         is_pairwise=False,
                         axes_labels=args.axes_ticks,
+                        axes_tick_number=args.axes_number,
+                        vector_format=args.vector,
+                        deraster=args.deraster,
                     )
 
         # -----------COMPUTE COMPARATIVE PLOTS-----------
         # TODO: Optimize computations so that largest sequence doesn't need to be redone all the time
-        if (args.compare or args.compare_only) and len(sequences) > 1:
+        if (args.compare or args.compare_only or args.grid or args.grid_only) and len(
+            sequences
+        ) > 1:
             # Set window size to args.window. Otherwise, set it to n/resolution
 
             if args.grid or args.grid_only:
                 grid_val_doubles = []
                 grid_val_double_names = []
+                xlim_val_grid = 0
 
             for i in range(len(sequences)):
                 for j in range(i + 1, len(sequences)):
@@ -1060,7 +1093,7 @@ def main():
                             grid_val_double_names.append(
                                 [larger_seq_name, smaller_seq_name]
                             )
-
+                            xlim_val_grid = max(larger_length, xlim_val_grid)
                         if not args.no_bed:
                             # Log saving bed file
                             if not args.output_dir:
@@ -1083,7 +1116,7 @@ def main():
                                     bedfile.write("\t".join(map(str, row)) + "\n")
                             print(f"Saved bed file to {bedfile_output}\n")
 
-                        if not args.no_plot:
+                        if (not args.no_plot) and (not args.grid_only):
                             create_plots(
                                 sdf=[bed],
                                 directory=args.output_dir if args.output_dir else ".",
@@ -1092,7 +1125,7 @@ def main():
                                 palette=args.palette,
                                 palette_orientation=args.palette_orientation,
                                 no_hist=args.no_hist,
-                                width=None,
+                                width=args.width,
                                 dpi=args.dpi,
                                 is_freq=args.bin_freq,
                                 xlim=args.axes_limits,
@@ -1101,6 +1134,9 @@ def main():
                                 from_file=None,
                                 is_pairwise=True,
                                 axes_labels=args.axes_ticks,
+                                axes_tick_number=args.axes_number,
+                                vector_format=args.vector,
+                                deraster=args.deraster,
                             )
 
             if args.grid or args.grid_only:
@@ -1111,15 +1147,18 @@ def main():
                     directory=args.output_dir if args.output_dir else ".",
                     palette=args.palette,
                     palette_orientation=args.palette_orientation,
-                    no_hist=args.no_hist,
                     single_names=grid_val_single_names,
                     double_names=grid_val_double_names,
                     is_freq=args.bin_freq,
-                    xlim=args.axes_limits,
+                    xlim=xlim_val_grid,
                     custom_colors=args.colors,
                     custom_breakpoints=args.axes_ticks,
                     axes_label=args.axes_ticks,
                     is_bed=False,
+                    width=args.width,
+                    breaks=args.axes_ticks,
+                    deraster=args.deraster,
+                    vector_format=args.vector,
                 )
 
 

{moddotplot-0.9.0 → moddotplot-0.9.1}/src/moddotplot/parse_fasta.py

@@ -7,6 +7,7 @@ import os
 import pickle
 import re
 import numpy as np
+import gzip
 
 tab_b = bytes.maketrans(b"ACTG", b"TGAC")
 
@@ -43,7 +44,8 @@ def generateKmersFromFasta(seq: Sequence[str], k: int, quiet: bool) -> Iterable[
 
 def isValidFasta(file_path):
     try:
-        with open(file_path, "r") as file:
+        open_func = gzip.open if file_path.endswith(".gz") else open
+        with open_func(file_path, "rt") as file:
             in_sequence = False
             for line in file:
                 line = line.strip()
@@ -144,7 +146,10 @@ def readKmersFromFile(filename: str, ksize: int, quiet: bool) -> List[List[int]]
 
 def getInputHeaders(filename: str) -> List[str]:
     header_list = []
-    seq = pysam.FastaFile(filename)
+    try:
+        seq = pysam.FastaFile(filename)
+    except OSError:
+        seq = None
     for seq_id in seq.references:
         header_list.append(seq_id)