Merge pull request #38 from marbl/develop

v0.9.0 release

Author: alexsweeten

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ModDotPlot"
-version = "0.8.8"
+version = "0.9.0"
 requires-python = ">= 3.7"
 dependencies = [
   "pysam",

src/moddotplot/const.py

@@ -1,4 +1,4 @@
-VERSION = "0.8.8"
+VERSION = "0.9.0"
 COLS = [
     "#query_name",
     "query_start",

src/moddotplot/moddotplot.py

@@ -21,7 +21,7 @@
 
 import argparse
 import math
-from moddotplot.static_plots import read_df_from_file, create_plots
+from moddotplot.static_plots import read_df_from_file, create_plots, create_grid
 import json
 import numpy as np
 import pickle
@@ -342,6 +342,12 @@ def get_parser():
         help="Plot comparative plots in an NxN grid like format.",
     )
 
+    static_parser.add_argument(
+        "--grid-only",
+        action="store_true",
+        help="Plot comparative plots in an NxN grid like format, skipping individual plots",
+    )
+
     # TODO: Implement static mode logging options
 
     return parser
@@ -428,6 +434,13 @@ def main():
                 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 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)
 
         # -----------INPUT COMMAND VALIDATION-----------
         # TODO: More tests!
@@ -447,65 +460,100 @@ def main():
 
         # -----------BEDFILE INPUT FOR STATIC MODE-----------
         if hasattr(args, "bed") and args.bed:
+            if args.grid or args.grid_only:
+                single_vals = []
+                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"]]
-                    print(
-                        f"Input bed file {bed} read successfully! Creating plots... \n"
-                    )
+                    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:
-                        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 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])
                     # Case 2: Pairwise bed file
                     if len(pairwise_id_scores) > 1:
-                        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,  # TODO: Get xlim working
-                            custom_colors=args.colors,
-                            custom_breakpoints=args.breakpoints,
-                            from_file=df,
-                            is_pairwise=True,
-                            axes_labels=args.axes_ticks,
-                        )
+                        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:
@@ -531,7 +579,6 @@ def main():
     for i in args.fasta:
         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.
     if len(k_list) < 2 and args.compare_only:
         print(
@@ -817,8 +864,12 @@ def main():
     # -----------SETUP STATIC MODE-----------
     elif args.command == "static":
         # -----------SET SPARSITY VALUE-----------
-        # TODO: this is not sorting correctly
+        if args.grid or args.grid_only:
+            grid_val_singles = []
+            grid_val_single_names = []
         sequences = list(zip(seq_list, k_list))
+        if len(sequences) > 6 and (args.grid or args.grid_only):
+            print("Too many sequences to create a grid. Skipping. \n")
 
         # Create output directory, if doesn't exist:
         if (args.output_dir) and not os.path.exists(args.output_dir):
@@ -884,6 +935,9 @@ def main():
                 bed = convertMatrixToBed(
                     self_mat, win, args.identity, seq_list[i], seq_list[i], True
                 )
+                if args.grid or args.grid_only:
+                    grid_val_singles.append(bed)
+                    grid_val_single_names.append(sequences[i][0])
 
                 if not args.no_bed:
                     # Log saving bed file
@@ -923,8 +977,9 @@ def main():
         if (args.compare or args.compare_only) and len(sequences) > 1:
             # Set window size to args.window. Otherwise, set it to n/resolution
 
-            if args.grid:
-                grid_vals = []
+            if args.grid or args.grid_only:
+                grid_val_doubles = []
+                grid_val_double_names = []
 
             for i in range(len(sequences)):
                 for j in range(i + 1, len(sequences)):
@@ -987,7 +1042,7 @@ def main():
                         expectation,
                     )
                     # Throw error if the matrix is empty
-                    if np.all(pair_mat == 0):
+                    if np.all(pair_mat == 0) and (not (args.grid or args.grid_only)):
                         print(
                             f"The pairwise identity matrix for {sequences[i][0]} and {sequences[j][0]} is empty. Skipping.\n"
                         )
@@ -1000,8 +1055,11 @@ def main():
                             seq_list[j],
                             False,
                         )
-                        if args.grid:
-                            grid_vals.append(bed)
+                        if args.grid or args.grid_only:
+                            grid_val_doubles.append(bed)
+                            grid_val_double_names.append(
+                                [larger_seq_name, smaller_seq_name]
+                            )
 
                         if not args.no_bed:
                             # Log saving bed file
@@ -1045,8 +1103,24 @@ def main():
                                 axes_labels=args.axes_ticks,
                             )
 
-            """if args.grid:
-                print(grid_vals)"""
+            if args.grid or args.grid_only:
+                print(f"Creating a {len(sequences)}x{len(sequences)} grid.\n")
+                create_grid(
+                    singles=grid_val_singles,
+                    doubles=grid_val_doubles,
+                    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,
+                    custom_colors=args.colors,
+                    custom_breakpoints=args.axes_ticks,
+                    axes_label=args.axes_ticks,
+                    is_bed=False,
+                )
 
 
 if __name__ == "__main__":