ModDotPlot 0.9.7__tar.gz → 0.9.9__tar.gz

{moddotplot-0.9.7/src/ModDotPlot.egg-info → moddotplot-0.9.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ModDotPlot
-Version: 0.9.7
+Version: 0.9.9
 Author: Michael Schatz, Adam Phillippy
 Author-email: Alex Sweeten <alex.sweeten@nih.gov>
 Maintainer-email: Alex Sweeten <alex.sweeten@nih.gov>
@@ -87,11 +87,11 @@ If you use ModDotPlot for your research, please cite our software!
 
 ## About
 
-_ModDotPlot_ is a dot plot visualization tool designed for large sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers, and rapidly approximating the Average Nucleotide Identity between pairwise combinations of these intervals. This significantly reduces the computational time required to produce these plots, enough to view multiple layers of resolution in real time!
+_ModDotPlot_ is a dot plot visualization tool designed to be used at scale, both for smaller sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers. This enables the rapid approximation of the Average Nucleotide Identity between combinations of intervals! 
 
 ![](images/demo.gif)
 
-If you're interested in learning more about ModDotPlot and tandem repeats, you can watch my in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) from the [BioDiversity Genomics Academy](https://thebgacademy.org).
+If you're interested in learning more about _ModDotPlot_ and how to visualize tandem repeats, we have an in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) hosted by the [BioDiversity Genomics Academy](https://thebgacademy.org).
 
 --- 
 
@@ -126,11 +126,11 @@ Finally, confirm that the installation was installed correctly and that your ver
  | |  | | (_) | (_| | | |__| | (_) | |_  | |    | | (_) | |_ 
  |_|  |_|\___/ \__,_| |_____/ \___/ \__| |_|    |_|\___/ \__|
 
- v0.9.7
+ v0.9.8
 
 usage: moddotplot [-h] {interactive,static} ...
 
-ModDotPlot: Visualization of Complex Repeat Structures
+ModDotPlot: Visualization of Tandem Repeats
 
 positional arguments:
   {interactive,static}  Choose mode: interactive or static
@@ -138,8 +138,11 @@ positional arguments:
     static              Static mode commands
 
 options:
-  -h, --help            show this help message and exit`
+  -h, --help            show this help message and exit
   ```
+
+Note that running `moddotplot -h` might take a while at first! This is because the Python interpreter is compiling source code into the __pycache__ directory. Subsequent runs will use the pre-compiled code and load much faster!
+
 --- 
 
 ## Usage
@@ -171,7 +174,7 @@ _ModDotPlot_ supports highly customizable plotting features in static mode. See
 moddotplot interactive <ARGS>
 ```
 
-Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info).
+Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info, and [Sample run - Port Forwarding](#sample-run---port-forwarding) for tips on running interactive mode on an HPC environment).
 
 --- 
 
@@ -207,6 +210,10 @@ Each partition takes into account a fraction of its neighboring partitions k-mer
 
 Modimizer sketch size. Must be lower than window size `w`. A lower sketch size means less k-mers to compare (and faster runtime), at the expense of lower accuracy. Recommended to be kept >= 1000.
 
+`--forward <bool>`
+
+Use forward k-mers only, instead of the default of canonical k-mers. Warning: this will give strand specific output.
+
 `-r / --resolution <int>`
 
 Dotplot resolution. This corresponds to the number of windows each input sequence is partitioned into. Default is 1000. Overrides the `--window` parameter.
@@ -275,9 +282,17 @@ By default, vectorized outputs rasterize the actual dotplot (not the axis). This
 
 Window size. Unlike interactive mode, only one matrix will be created, so this represents the *only* window size. Default is set to `n/1000` (eg. 3000bp for a 3Mbp sequence). 
 
+`--region <list of strs>`
+
+Plot only a particular range for a given sequence. Syntax is UCSC style (chr:start-end).
+
 `--palette <str>`
 
-List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). The syntax is to have the name of the palette, followed by an underscore with the number of colors, eg. `OrRd_8`. Default is `Spectral_11`.
+List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). Palettes are segregated into 3 types: _Diverging_, _Qualitative_, and _Sequential_. Syntax is the name of the palette, followed by an underscore and the number of colors, eg. `OrRd_8`. Default is  `Spectral_11`.
+
+`--breakpoints <list of ints>`
+
+Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1, otherwise an error will occur. 
 
 `--palette-orientation <bool>`
 
@@ -287,10 +302,6 @@ Flip sequential order of color palette. Set to `-` by default for divergent pale
 
 List of custom colors in hexcode format can be entered sequentially, mapped from low to high identity. 
 
-`--breakpoints <list of ints>`
-
-Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1.
-
 `-t / --axes-ticks <list of ints>`
 
 Custom tickmarks for x and y axis. Values outside of the `--axes-limits` will not be shown. 
@@ -515,3 +526,5 @@ For bug reports or general usage questions, please raise a GitHub issue, or emai
 - 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`. 
+
+- The error ` UserWarning: h5py is running against HDF5 1.xx.x when it was built against 1.xx.x, this may cause problems` is due to the h5py library used by cooler having conflicting versions in the dependency tree. This can also be safely ignored, but if you want to remove this message run `pip uninstall -y h5py` `pip install --no-binary=h5py h5py`

{moddotplot-0.9.7 → moddotplot-0.9.9}/README.md

@@ -35,11 +35,11 @@ If you use ModDotPlot for your research, please cite our software!
 
 ## About
 
-_ModDotPlot_ is a dot plot visualization tool designed for large sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers, and rapidly approximating the Average Nucleotide Identity between pairwise combinations of these intervals. This significantly reduces the computational time required to produce these plots, enough to view multiple layers of resolution in real time!
+_ModDotPlot_ is a dot plot visualization tool designed to be used at scale, both for smaller sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers. This enables the rapid approximation of the Average Nucleotide Identity between combinations of intervals! 
 
 ![](images/demo.gif)
 
-If you're interested in learning more about ModDotPlot and tandem repeats, you can watch my in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) from the [BioDiversity Genomics Academy](https://thebgacademy.org).
+If you're interested in learning more about _ModDotPlot_ and how to visualize tandem repeats, we have an in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) hosted by the [BioDiversity Genomics Academy](https://thebgacademy.org).
 
 --- 
 
@@ -74,11 +74,11 @@ Finally, confirm that the installation was installed correctly and that your ver
  | |  | | (_) | (_| | | |__| | (_) | |_  | |    | | (_) | |_ 
  |_|  |_|\___/ \__,_| |_____/ \___/ \__| |_|    |_|\___/ \__|
 
- v0.9.7
+ v0.9.8
 
 usage: moddotplot [-h] {interactive,static} ...
 
-ModDotPlot: Visualization of Complex Repeat Structures
+ModDotPlot: Visualization of Tandem Repeats
 
 positional arguments:
   {interactive,static}  Choose mode: interactive or static
@@ -86,8 +86,11 @@ positional arguments:
     static              Static mode commands
 
 options:
-  -h, --help            show this help message and exit`
+  -h, --help            show this help message and exit
   ```
+
+Note that running `moddotplot -h` might take a while at first! This is because the Python interpreter is compiling source code into the __pycache__ directory. Subsequent runs will use the pre-compiled code and load much faster!
+
 --- 
 
 ## Usage
@@ -119,7 +122,7 @@ _ModDotPlot_ supports highly customizable plotting features in static mode. See
 moddotplot interactive <ARGS>
 ```
 
-Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info).
+Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info, and [Sample run - Port Forwarding](#sample-run---port-forwarding) for tips on running interactive mode on an HPC environment).
 
 --- 
 
@@ -155,6 +158,10 @@ Each partition takes into account a fraction of its neighboring partitions k-mer
 
 Modimizer sketch size. Must be lower than window size `w`. A lower sketch size means less k-mers to compare (and faster runtime), at the expense of lower accuracy. Recommended to be kept >= 1000.
 
+`--forward <bool>`
+
+Use forward k-mers only, instead of the default of canonical k-mers. Warning: this will give strand specific output.
+
 `-r / --resolution <int>`
 
 Dotplot resolution. This corresponds to the number of windows each input sequence is partitioned into. Default is 1000. Overrides the `--window` parameter.
@@ -223,9 +230,17 @@ By default, vectorized outputs rasterize the actual dotplot (not the axis). This
 
 Window size. Unlike interactive mode, only one matrix will be created, so this represents the *only* window size. Default is set to `n/1000` (eg. 3000bp for a 3Mbp sequence). 
 
+`--region <list of strs>`
+
+Plot only a particular range for a given sequence. Syntax is UCSC style (chr:start-end).
+
 `--palette <str>`
 
-List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). The syntax is to have the name of the palette, followed by an underscore with the number of colors, eg. `OrRd_8`. Default is `Spectral_11`.
+List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). Palettes are segregated into 3 types: _Diverging_, _Qualitative_, and _Sequential_. Syntax is the name of the palette, followed by an underscore and the number of colors, eg. `OrRd_8`. Default is  `Spectral_11`.
+
+`--breakpoints <list of ints>`
+
+Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1, otherwise an error will occur. 
 
 `--palette-orientation <bool>`
 
@@ -235,10 +250,6 @@ Flip sequential order of color palette. Set to `-` by default for divergent pale
 
 List of custom colors in hexcode format can be entered sequentially, mapped from low to high identity. 
 
-`--breakpoints <list of ints>`
-
-Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1.
-
 `-t / --axes-ticks <list of ints>`
 
 Custom tickmarks for x and y axis. Values outside of the `--axes-limits` will not be shown. 
@@ -463,3 +474,5 @@ For bug reports or general usage questions, please raise a GitHub issue, or emai
 - 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`. 
+
+- The error ` UserWarning: h5py is running against HDF5 1.xx.x when it was built against 1.xx.x, this may cause problems` is due to the h5py library used by cooler having conflicting versions in the dependency tree. This can also be safely ignored, but if you want to remove this message run `pip uninstall -y h5py` `pip install --no-binary=h5py h5py`

{moddotplot-0.9.7 → moddotplot-0.9.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ModDotPlot"
-version = "0.9.7"
+version = "0.9.9"
 requires-python = ">= 3.7"
 dependencies = [
   "pysam",

{moddotplot-0.9.7 → moddotplot-0.9.9/src/ModDotPlot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ModDotPlot
-Version: 0.9.7
+Version: 0.9.9
 Author: Michael Schatz, Adam Phillippy
 Author-email: Alex Sweeten <alex.sweeten@nih.gov>
 Maintainer-email: Alex Sweeten <alex.sweeten@nih.gov>
@@ -87,11 +87,11 @@ If you use ModDotPlot for your research, please cite our software!
 
 ## About
 
-_ModDotPlot_ is a dot plot visualization tool designed for large sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers, and rapidly approximating the Average Nucleotide Identity between pairwise combinations of these intervals. This significantly reduces the computational time required to produce these plots, enough to view multiple layers of resolution in real time!
+_ModDotPlot_ is a dot plot visualization tool designed to be used at scale, both for smaller sequences and whole genomes. _ModDotPlot_ is the spiritual successor to [StainedGlass](https://mrvollger.github.io/StainedGlass/). The core algorithm breaks an input sequence down into intervals of sketched *k*-mers called **mod**imizers. This enables the rapid approximation of the Average Nucleotide Identity between combinations of intervals! 
 
 ![](images/demo.gif)
 
-If you're interested in learning more about ModDotPlot and tandem repeats, you can watch my in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) from the [BioDiversity Genomics Academy](https://thebgacademy.org).
+If you're interested in learning more about _ModDotPlot_ and how to visualize tandem repeats, we have an in-depth [YouTube video tutorial](https://www.youtube.com/watch?v=_7sQaljB_ys&t=2321s&pp=ygUXYWxleCBzd2VldGVuIG1vZGRvdHBsb3Q%3D) hosted by the [BioDiversity Genomics Academy](https://thebgacademy.org).
 
 --- 
 
@@ -126,11 +126,11 @@ Finally, confirm that the installation was installed correctly and that your ver
  | |  | | (_) | (_| | | |__| | (_) | |_  | |    | | (_) | |_ 
  |_|  |_|\___/ \__,_| |_____/ \___/ \__| |_|    |_|\___/ \__|
 
- v0.9.7
+ v0.9.8
 
 usage: moddotplot [-h] {interactive,static} ...
 
-ModDotPlot: Visualization of Complex Repeat Structures
+ModDotPlot: Visualization of Tandem Repeats
 
 positional arguments:
   {interactive,static}  Choose mode: interactive or static
@@ -138,8 +138,11 @@ positional arguments:
     static              Static mode commands
 
 options:
-  -h, --help            show this help message and exit`
+  -h, --help            show this help message and exit
   ```
+
+Note that running `moddotplot -h` might take a while at first! This is because the Python interpreter is compiling source code into the __pycache__ directory. Subsequent runs will use the pre-compiled code and load much faster!
+
 --- 
 
 ## Usage
@@ -171,7 +174,7 @@ _ModDotPlot_ supports highly customizable plotting features in static mode. See
 moddotplot interactive <ARGS>
 ```
 
-Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info).
+Running _ModDotPlot_ in interactive mode will launch a [Dash application](https://plotly.com/dash/) on your machine's localhost. Open any web browser and go to `http://127.0.0.1:<PORT_NUMBER>` to view the interactive plot (this should happen automatically, but depending on your environment you might need to copy and paste this URL into your web browser). Running `Ctrl+C` on the command line will exit the Dash application. The default port number used by Dash is `8050`, but this can be customized using the `--port` command (see [interactive mode commands](#interactive-mode-commands) for further info, and [Sample run - Port Forwarding](#sample-run---port-forwarding) for tips on running interactive mode on an HPC environment).
 
 --- 
 
@@ -207,6 +210,10 @@ Each partition takes into account a fraction of its neighboring partitions k-mer
 
 Modimizer sketch size. Must be lower than window size `w`. A lower sketch size means less k-mers to compare (and faster runtime), at the expense of lower accuracy. Recommended to be kept >= 1000.
 
+`--forward <bool>`
+
+Use forward k-mers only, instead of the default of canonical k-mers. Warning: this will give strand specific output.
+
 `-r / --resolution <int>`
 
 Dotplot resolution. This corresponds to the number of windows each input sequence is partitioned into. Default is 1000. Overrides the `--window` parameter.
@@ -275,9 +282,17 @@ By default, vectorized outputs rasterize the actual dotplot (not the axis). This
 
 Window size. Unlike interactive mode, only one matrix will be created, so this represents the *only* window size. Default is set to `n/1000` (eg. 3000bp for a 3Mbp sequence). 
 
+`--region <list of strs>`
+
+Plot only a particular range for a given sequence. Syntax is UCSC style (chr:start-end).
+
 `--palette <str>`
 
-List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). The syntax is to have the name of the palette, followed by an underscore with the number of colors, eg. `OrRd_8`. Default is `Spectral_11`.
+List of accepted palettes can be found [here](https://jiffyclub.github.io/palettable/colorbrewer/). Palettes are segregated into 3 types: _Diverging_, _Qualitative_, and _Sequential_. Syntax is the name of the palette, followed by an underscore and the number of colors, eg. `OrRd_8`. Default is  `Spectral_11`.
+
+`--breakpoints <list of ints>`
+
+Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1, otherwise an error will occur. 
 
 `--palette-orientation <bool>`
 
@@ -287,10 +302,6 @@ Flip sequential order of color palette. Set to `-` by default for divergent pale
 
 List of custom colors in hexcode format can be entered sequentially, mapped from low to high identity. 
 
-`--breakpoints <list of ints>`
-
-Add custom identity threshold breakpoints. Note that the number of breakpoints must be equal to the number of colors + 1.
-
 `-t / --axes-ticks <list of ints>`
 
 Custom tickmarks for x and y axis. Values outside of the `--axes-limits` will not be shown. 
@@ -515,3 +526,5 @@ For bug reports or general usage questions, please raise a GitHub issue, or emai
 - 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`. 
+
+- The error ` UserWarning: h5py is running against HDF5 1.xx.x when it was built against 1.xx.x, this may cause problems` is due to the h5py library used by cooler having conflicting versions in the dependency tree. This can also be safely ignored, but if you want to remove this message run `pip uninstall -y h5py` `pip install --no-binary=h5py h5py`

{moddotplot-0.9.7 → moddotplot-0.9.9}/src/moddotplot/const.py

@@ -1,4 +1,4 @@
-VERSION = "0.9.7"
+VERSION = "0.9.9"
 COLS = [
     "#query_name",
     "query_start",

{moddotplot-0.9.7 → moddotplot-0.9.9}/src/moddotplot/estimate_identity.py

@@ -141,8 +141,10 @@ def partitionOverlaps(
         kmer_list.append(lst[final_start_index:seq_len])
 
     # Test that last value was added on correctly
-
-    assert kmer_list[-1][-1] == lst[-1]
+    try:
+        assert kmer_list[-1][-1] == lst[-1]
+    except (AssertionError, IndexError) as e:
+        print(f"Error: Last k-mer does not match original sequence: {e}\n")
     return kmer_list
 
 
@@ -352,6 +354,9 @@ def selfContainmentMatrix(
     n = len(mod_set)
     progress_thresholds = round(n / 77)
 
+    if progress_thresholds == 0:
+        progress_thresholds = 1
+
     printProgressBar(0, n, prefix="Progress:", suffix="Complete", length=40)
     containment_matrix = np.empty((n, n))
 
@@ -410,6 +415,8 @@ def pairwiseContainmentMatrix(
     """
     n = max(len(mod_set_y), len(mod_set_x))
     progress_thresholds = round(n / 77)
+    if progress_thresholds == 0:
+        progress_thresholds = 1
 
     if not supress_progress:
         printProgressBar(0, n, prefix="Progress:", suffix="Complete", length=40)

{moddotplot-0.9.7 → moddotplot-0.9.9}/src/moddotplot/moddotplot.py

@@ -28,7 +28,6 @@ import json
 import numpy as np
 import pickle
 import os
-import cooler
 
 
 def get_parser():
@@ -230,6 +229,13 @@ def get_parser():
         help="Window size, or the length in genomic coordinates of each interval. Default is set to (genome length)/(resolution)",
     )
 
+    static_parser.add_argument(
+        "--region",
+        default=None,
+        help="Genomic region to analyze. Syntax is seq_id:start-end (e.g. chr1:100000-200000).",
+        nargs="+",
+    )
+
     static_parser.add_argument(
         "-id",
         "--identity",
@@ -310,6 +316,18 @@ def get_parser():
         type=str,
     )
 
+    static_parser.add_argument(
+        "--forward",
+        action="store_true",
+        help="Enforce forward only k-mers instead of canonical k-mers. Warning: only use if you want strand-specific output!",
+    )
+
+    static_parser.add_argument(
+        "--plot-direction",
+        action="store_true",
+        help="Create a plot containing the direction of each k-mer array (relative to the first array). Arrays with inversions will be highlighted in blue (forward) and pink (reverse).",
+    )
+
     static_parser.add_argument(
         "--colors",
         default=None,
@@ -405,7 +423,6 @@ def main():
             axes = []
             for i in range(len(matrices)):
                 matrix_axes = []
-                counter = 0
                 for matrix in matrices[i]:
                     x_axis = [
                         j * round(metadata[i]["x_size"] / matrix.shape[0])
@@ -630,7 +647,10 @@ def main():
     # -----------LOAD SEQUENCES INTO MEMORY-----------
     kmer_list = []
     for i in fasta_list:
-        kmer_list.append(readKmersFromFile(i, args.kmer, False))
+        if args.forward:
+            kmer_list.append(readKmersFromFile(i, args.kmer, False, True))
+        else:
+            kmer_list.append(readKmersFromFile(i, args.kmer, False, 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:
@@ -937,6 +957,48 @@ def main():
                 seq_length = len(sequences[i][1])
                 seq_name = sequences[i][0]
                 seq_range = extractRegion(seq_name)
+                if seq_range:
+                    seq_name = seq_range[0]
+                # If region, then I only want to use the subsequence.
+                try:
+                    if args.region:
+                        subseq_start_pos = None
+                        subseq_end_pos = None
+                        for region in args.region:
+                            chrom, lower_bound, upper_bound = extractRegion(region)
+                            if chrom == seq_name:
+                                subseq_start_pos = lower_bound
+                                subseq_end_pos = upper_bound
+                                seq_start_pos = lower_bound
+                                # Validate bounds
+                                if subseq_start_pos < 1 or subseq_end_pos > seq_length:
+                                    print(
+                                        f"Error: region {region} is out of bounds for {seq_name}. Will use entire sequence.\n"
+                                    )
+                                    subseq_start_pos = 1
+                                    subseq_end_pos = seq_length
+                                    seq_name = sequences[i][0]
+                                    break
+                                print(
+                                    f"Using region {seq_name}:{subseq_start_pos}-{subseq_end_pos}\n"
+                                )
+                                # Change sequence length, and use a subsequence instead.
+                                seq_length = (
+                                    subseq_end_pos - subseq_start_pos + 1 - args.kmer
+                                )
+                                seq_range = seq_name, subseq_start_pos, subseq_end_pos
+                                seq_name = (
+                                    f"{seq_name}:{subseq_start_pos}-{subseq_end_pos}"
+                                )
+                        if not subseq_end_pos or not subseq_start_pos:
+                            print(
+                                f"Error: region {args.region} not found in {seq_name}. Will use entire sequence.\n"
+                            )
+                            seq_range = None
+                except Exception as e:
+                    print(
+                        f"Error obtaining region for {seq_name}. Will use entire sequence: {e}\n"
+                    )
                 if not seq_range:
                     seq_start_pos = 1
                 else:
@@ -972,17 +1034,33 @@ def main():
                 print(f"\tWindow size w: {win}\n")
                 print(f"\tModimizer sketch size: {expectation}\n")
                 print(f"\tPlot Resolution r: {res}\n")
-                self_mat = createSelfMatrix(
-                    seq_length,
-                    sequences[i][1],
-                    win,
-                    seq_sparsity,
-                    args.delta,
-                    args.kmer,
-                    args.identity,
-                    args.ambiguous,
-                    expectation,
-                )
+                if args.region and seq_range:
+                    subseq = sequences[i][1][
+                        subseq_start_pos : (subseq_end_pos - args.kmer + 1)
+                    ]
+                    self_mat = createSelfMatrix(
+                        seq_length,
+                        subseq,
+                        win,
+                        seq_sparsity,
+                        args.delta,
+                        args.kmer,
+                        args.identity,
+                        args.ambiguous,
+                        expectation,
+                    )
+                else:
+                    self_mat = createSelfMatrix(
+                        seq_length,
+                        sequences[i][1],
+                        win,
+                        seq_sparsity,
+                        args.delta,
+                        args.kmer,
+                        args.identity,
+                        args.ambiguous,
+                        expectation,
+                    )
                 bed = convertMatrixToBed(
                     self_mat,
                     win,
@@ -1093,11 +1171,96 @@ def main():
                         larger_seq_start_pos = 1
                     else:
                         larger_seq_start_pos = int(larger_seq_range[1])
+                        larger_seq_name = larger_seq_range[0]
                     smaller_seq_range = extractRegion(smaller_seq_name)
-                    if not larger_seq_range:
+                    if not smaller_seq_range:
                         smaller_seq_start_pos = 1
                     else:
                         smaller_seq_start_pos = int(smaller_seq_range[1])
+                        smaller_seq_name = smaller_seq_range[0]
+
+                    try:
+                        if args.region:
+                            subseq_start_pos = None
+                            subseq_end_pos = None
+                            for region in args.region:
+                                chrom, lower_bound, upper_bound = extractRegion(region)
+                                if chrom == larger_seq_name:
+                                    larger_subseq_start_pos = lower_bound
+                                    larger_subseq_end_pos = upper_bound
+                                    larger_seq_start_pos = lower_bound
+                                    # Validate bounds
+                                    if (
+                                        larger_seq_start_pos < 1
+                                        or larger_subseq_end_pos > larger_length
+                                    ):
+                                        print(
+                                            f"Error: region {region} is out of bounds for {larger_seq_name}. Will use entire sequence.\n"
+                                        )
+                                        larger_subseq_start_pos = 1
+                                        larger_subseq_end_pos = larger_length
+                                        larger_seq_name = sequences[i][0]
+                                        break
+                                    print(
+                                        f"Using region {larger_seq_name}:{larger_subseq_start_pos}-{larger_subseq_end_pos}\n"
+                                    )
+                                    # Change sequence length, and use a subsequence instead.
+                                    larger_length = (
+                                        larger_subseq_end_pos
+                                        - larger_subseq_start_pos
+                                        + 1
+                                        - args.kmer
+                                    )
+                                    larger_seq_range = (
+                                        larger_seq_name,
+                                        larger_subseq_start_pos,
+                                        larger_subseq_end_pos,
+                                    )
+                                    larger_seq_name = f"{larger_seq_name}:{larger_subseq_start_pos}-{larger_subseq_end_pos}"
+
+                                if chrom == smaller_seq_name:
+                                    smaller_subseq_start_pos = lower_bound
+                                    smaller_subseq_end_pos = upper_bound
+                                    smaller_seq_start_pos = lower_bound
+                                    # Validate bounds
+                                    if (
+                                        smaller_seq_start_pos < 1
+                                        or smaller_subseq_end_pos > smaller_length
+                                    ):
+                                        print(
+                                            f"Error: region {region} is out of bounds for {smaller_seq_name}. Will use entire sequence.\n"
+                                        )
+                                        smaller_subseq_start_pos = 1
+                                        smaller_subseq_end_pos = smaller_length
+                                        smaller_seq_name = sequences[j][0]
+                                        break
+                                    print(
+                                        f"Using region {smaller_seq_name}:{smaller_subseq_start_pos}-{smaller_subseq_end_pos}\n"
+                                    )
+                                    # Change sequence length, and use a subsequence instead.
+                                    smaller_length = (
+                                        smaller_subseq_end_pos
+                                        - smaller_subseq_start_pos
+                                        + 1
+                                        - args.kmer
+                                    )
+                                    smaller_seq_range = (
+                                        smaller_seq_name,
+                                        smaller_subseq_start_pos,
+                                        smaller_subseq_end_pos,
+                                    )
+                                    smaller_seq_name = f"{smaller_seq_name}:{smaller_subseq_start_pos}-{smaller_subseq_end_pos}"
+                            # This is wrong. Might be fine to leave alone
+                            if not larger_subseq_end_pos or not larger_subseq_start_pos:
+                                print(
+                                    f"Error: region {args.region} not found in {seq_name}. Will use entire sequence.\n"
+                                )
+                                seq_range = None
+                    except Exception as e:
+                        print(
+                            f"Error obtaining region for {seq_name}. Will use entire sequence: {e}\n"
+                        )
+
                     win = args.window
                     res = args.resolution
                     if args.window:
@@ -1117,7 +1280,6 @@ def main():
                         f"Computing pairwise identity matrix for {larger_seq_name} and {smaller_seq_name}... \n"
                     )
                     # TODO: Logging here
-                    # print(f"\tSparsity value s: {seq_sparsity}\n")
                     print(
                         f"\tSequence length {larger_seq_name}: {larger_length + args.kmer - 1}\n"
                     )
@@ -1128,19 +1290,52 @@ def main():
                     print(f"\tModimizer sketch size: {expectation}\n")
                     print(f"\tPlot Resolution r: {res}\n")
 
-                    pair_mat = createPairwiseMatrix(
-                        smaller_length,
-                        larger_length,
-                        smaller_seq,
-                        larger_seq,
-                        win,
-                        seq_sparsity,
-                        args.delta,
-                        args.kmer,
-                        args.identity,
-                        args.ambiguous,
-                        expectation,
-                    )
+                    if args.region and (larger_seq_range or smaller_seq_range):
+                        if larger_seq_range:
+                            larger_subseq = larger_seq[
+                                larger_subseq_start_pos : (
+                                    larger_subseq_end_pos - args.kmer + 1
+                                )
+                            ]
+                        else:
+                            larger_subseq = larger_seq
+
+                        if smaller_seq_range:
+                            smaller_subseq = smaller_seq[
+                                smaller_subseq_start_pos : (
+                                    smaller_subseq_end_pos - args.kmer + 1
+                                )
+                            ]
+                        else:
+                            smaller_subseq = smaller_seq
+
+                        pair_mat = createPairwiseMatrix(
+                            smaller_length,
+                            larger_length,
+                            smaller_subseq,
+                            larger_subseq,
+                            win,
+                            seq_sparsity,
+                            args.delta,
+                            args.kmer,
+                            args.identity,
+                            args.ambiguous,
+                            expectation,
+                        )
+                    else:
+                        pair_mat = createPairwiseMatrix(
+                            smaller_length,
+                            larger_length,
+                            smaller_seq,
+                            larger_seq,
+                            win,
+                            seq_sparsity,
+                            args.delta,
+                            args.kmer,
+                            args.identity,
+                            args.ambiguous,
+                            expectation,
+                        )
                     # Throw error if the matrix is empty
                     if np.all(pair_mat == 0) and (not (args.grid or args.grid_only)):
                         print(

{moddotplot-0.9.7 → moddotplot-0.9.9}/src/moddotplot/parse_fasta.py

@@ -13,24 +13,33 @@ tab_b = bytes.maketrans(b"ACTG", b"TGAC")
 
 
 def extractRegion(seq_name):
-    """Check if seq_name contains a region and extract the bounds."""
-    # Define the regular expression to match the format "chrY:50-3000"
-    region_pattern = r"([a-zA-Z0-9]+):(\d+)-(\d+)"
+    """Extract chromosome and region from seq_name.
+
+    Supports:
+    - Standard format: "chrY:50-3000"
+    - Extended format: "HG002_chr13_MATERNAL:1-4000000:1000000-3000000"
+      (keeps the last range).
+    """
+    # Match chromosome + one or more ranges separated by colons
+    region_pattern = r"^([a-zA-Z0-9_]+)(?::(\d+-\d+))+"
 
     match = re.match(region_pattern, seq_name)
     if match:
-        # Extract chromosome, lower bound, and upper bound
         chrom = match.group(1)
-        lower_bound = int(match.group(2))
-        upper_bound = int(match.group(3))
+        # Get all ranges (everything after the chrom)
+        ranges = re.findall(r"(\d+)-(\d+)", seq_name)
+        if ranges:
+            # Take the last range
+            lower_bound, upper_bound = map(int, ranges[-1])
+            return chrom, lower_bound, upper_bound
 
-        return chrom, lower_bound, upper_bound
-    else:
-        # No region found
-        return None
+    # No match
+    return None
 
 
-def generateKmersFromFasta(seq: Sequence[str], k: int, quiet: bool) -> Iterable[int]:
+def generateKmersFromFasta(
+    seq: Sequence[str], k: int, quiet: bool, fw_only: bool
+) -> Iterable[int]:
     n = len(seq)
     if not quiet:
         progress_thresholds = round(n / 77)
@@ -53,11 +62,12 @@ def generateKmersFromFasta(seq: Sequence[str], k: int, quiet: bool) -> Iterable[
         # Remove case sensitivity
         kmer = seq[i : i + k].upper()
         fh = mmh3.hash(kmer)
-
-        # Calculate reverse complement hash directly without the need for translation
-        rc = mmh3.hash(kmer[::-1].translate(tab_b))
-
-        yield fh if fh < rc else rc
+        if fw_only:
+            yield fh
+        else:
+            # Calculate reverse complement hash directly without the need for translation
+            rc = mmh3.hash(kmer[::-1].translate(tab_b))
+            yield fh if fh < rc else rc
 
 
 def isValidFasta(file_path):
@@ -144,7 +154,9 @@ def printProgressBar(
         print()
 
 
-def readKmersFromFile(filename: str, ksize: int, quiet: bool) -> List[List[int]]:
+def readKmersFromFile(
+    filename: str, ksize: int, quiet: bool, fw_only: bool
+) -> List[List[int]]:
     """
     Given a filename and an integer k, returns a list of all k-mers found in the sequences in the file.
     """
@@ -154,7 +166,9 @@ def readKmersFromFile(filename: str, ksize: int, quiet: bool) -> List[List[int]]
     for seq_id in seq.references:
         print(f"Retrieving k-mers from {seq_id}.... \n")
         kmers_for_seq = []
-        for kmer_hash in generateKmersFromFasta(seq.fetch(seq_id), ksize, quiet):
+        for kmer_hash in generateKmersFromFasta(
+            seq.fetch(seq_id), ksize, quiet, fw_only
+        ):
             kmers_for_seq.append(kmer_hash)
         all_kmers.append(kmers_for_seq)
         print(f"\n{seq_id} k-mers retrieved! \n")

{moddotplot-0.9.7 → moddotplot-0.9.9}/src/moddotplot/static_plots.py

@@ -1980,6 +1980,11 @@ def create_plots(
                 )
                 if os.path.exists(f"{anno_prefix}.svg"):
                     os.remove(f"{anno_prefix}.svg")
+                cairosvg.svg2png(
+                    url=f"{tri_prefix}_ANNOTATED.svg",
+                    write_to=f"{tri_prefix}_ANNOTATED.png",
+                    dpi=dpi,
+                )
                 try:
                     if vector_format != "svg":
                         if vector_format == "pdf":