Merge branch 'CW-2260-ezchart' into 'dev'

CW-2260 ezcharts report

Closes CW-2260

See merge request epi2melabs/workflows/wf-clone-validation!138

CHANGELOG.md

@@ -4,14 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
+## [v0.5.0]
+### Changed
+- The report has been updated and re-ordered to improve usability.
+- Default basecaller cfg is now `dna_r10.4.1_e8.2_400bps_sup@v4.2.0`.
+- Docker will use an ARM platform image on appropriate devices.
 ### Fixed
 - Updated basecaller cfg model options.
 - Workflow will still output report if there are no assemblies.
 
-### Changed
-- Default basecaller cfg is now `dna_r10.4.1_e8.2_400bps_sup@v4.2.0`.
-
 ## [v0.4.0]
 ### Added
 - Documentation updated to include workflow steps.

bin/workflow_glue/bokeh_plot.py

@@ -0,0 +1,196 @@
+"""Script from plannotate edited to work with bokeh 3."""
+from math import pi
+
+from bokeh.models import ColumnDataSource, HoverTool, Range1d, WheelZoomTool
+from bokeh.models.annotations import Label
+from bokeh.plotting import figure
+import numpy as np
+import pandas as pd
+from plannotate.bokeh_plot import calc_glyphs, calc_level, calc_num_markers
+import plannotate.resources as rsc
+
+
+def get_bokeh(df, linear=False):
+    """Get bokeh from plannotate updated to use Bokeh v3 to match ezcharts."""
+    # df = df.fillna("")
+    x = 0
+    y = 0
+    baseradius = .18
+    tooltips = """
+            <font size="4"><b>@Feature</b> — @Type   @pi_permatch_int</font><br>
+            @Description
+    """  # noqa: E501
+    hover = HoverTool(tooltips=tooltips)
+    plotsize = .35
+    plotdimen = 800
+    x_range = Range1d(-plotsize, plotsize, bounds=(-.5, .5), min_interval=.1)
+    y_range = Range1d(-plotsize, plotsize, bounds=(-.5, .5), min_interval=.1)
+    toolbar = "right"
+    p = figure(
+        height=plotdimen, width=plotdimen, title="",
+        toolbar_location=toolbar, toolbar_sticky=False,
+        match_aspect=True,
+        sizing_mode='scale_width', tools=['save', 'pan'],
+        x_range=x_range, y_range=y_range)
+
+    # x_range=(-plotsize, plotsize), y_range=(-plotsize, plotsize))
+    p.toolbar.logo = None
+    p.add_tools(WheelZoomTool(zoom_on_axis=False))
+    p.toolbar.active_scroll = p.select_one(WheelZoomTool)
+
+    # backbone line
+    p.circle(
+        x=x, y=y, radius=baseradius, line_color="#000000",
+        fill_color=None, line_width=2.5)
+
+    df = calc_level(df)
+
+    if linear:
+        line_length = baseradius / 5
+        p.line(
+            [0, 0], [baseradius - line_length, baseradius + line_length],
+            line_width=4, level="overlay", line_color="black")
+
+    df['pi_permatch_int'] = df['pi_permatch'].astype('int')
+
+    df['pi_permatch_int'] = df['pi_permatch_int'].astype(str) + "%"
+    # removes percent from infernal hits
+    df.loc[df['db'] == "Rfam", 'pi_permatch_int'] = ""
+
+    df['rstart'] = ((df["qstart"]/df["qlen"])*2*pi)
+    df['rend'] = ((df["qend"]/df["qlen"])*2*pi)
+    df['rstart'] = np.where(
+        df['rstart'] < 0, df['rstart'] + (2*pi), df['rstart'])
+    df['rend'] = np.where(df['rend'] < 0, df['rend'] + (2*pi), df['rend'])
+    df['rend'] = np.where(
+        df['rend'] < df['rstart'], df['rend'] + (2*pi), df['rend'])
+
+    df['Type'] = df['Type'].str.replace('rep_origin', 'origin of replication')
+
+    # DDE0BD
+    # C97064
+    # C9E4CA
+    fullcolordf = pd.read_csv(
+        rsc.get_resource("data", "colors.csv"), index_col=0)
+    fragcolordf = fullcolordf.copy()
+    fragcolordf[['fill_color', 'line_color']] = fragcolordf[
+        ['line_color', 'fill_color']]
+    fragcolordf["fill_color"] = "#ffffff"
+
+    full = df[df["fragment"] == False] # noqa
+
+    full = full.merge(
+        fullcolordf,
+        how="left", on=["Type"])
+    full['legend'] = full['Type']
+    full = full.fillna(
+        {"color": "grey",
+         "fill_color": "#808080",
+         "line_color": "#000000"})
+    frag = df[df["fragment"]]
+    frag = frag.merge(fragcolordf, how="left", on=["Type"])
+    frag = frag.fillna(
+        {"color": "grey",
+         "fill_color": "#ffffff",
+         "line_color": "#808080"})
+
+    df = full.append(frag).reset_index(drop=True)
+
+    # add orientation column
+    orient = pd.read_csv(
+        rsc.get_resource("data", "feature_orientation.csv"),
+        header=None, names=["Type", "has_orientation"])
+    orient['Type'] = orient['Type']
+    orient['has_orientation'] = orient['has_orientation'].map({"T": True})
+    df = df.merge(orient, on="Type", how="left")
+    df['Type'] = df['Type'].str.replace("_", " ")
+    df['has_orientation'] = df['has_orientation'].fillna(value=False)
+    df[[
+        'x', 'y', "Lx1", "Ly1",
+        "annoLineColor", "lineX",
+        "lineY", "theta", "text_align"]] = df.apply(calc_glyphs, axis=1)
+    df['legend'] = df['Type']
+    # allowedtypes = ['CDS',"promoter","origin of replication","swissprot"]
+    allowedtypes = fullcolordf['Type']
+    mask = ~df['legend'].isin(allowedtypes)
+    df.loc[mask, 'legend'] = 'misc feature'
+
+    # plot annotations
+    source = ColumnDataSource(df)
+    hover_labels = p.patches(
+        'x', 'y', fill_color='fill_color', line_color='line_color',
+        name="features", line_width=2.5,
+        source=source, legend_group="legend")
+    p.multi_line(
+        xs="lineX", ys="lineY", line_color="annoLineColor",
+        line_width=3, level="overlay",
+        line_cap='round', alpha=.5, source=source)
+
+    # `text_align` cannot read from `source` -- have to do this workaround
+    right = ColumnDataSource(df[df['text_align'] == 'right'])
+    left = ColumnDataSource(df[df['text_align'] == 'left'])
+    bcenter = ColumnDataSource(df[df['text_align'] == 'b_center'])
+    tcenter = ColumnDataSource(df[df['text_align'] == 't_center'])
+
+    text_level = 'overlay'
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=3, y_offset=8,
+        text_align="left",
+        text='Feature', level=text_level, source=right)
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=-5, y_offset=8,
+        text_align="right", text='Feature', level=text_level, source=left)
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=15,
+        text_align="center", text='Feature',
+        level=text_level, source=bcenter)
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=0,
+        text_align="center",
+        text='Feature', level=text_level, source=tcenter)
+
+    # calculate chunk size(s) for drawing lines
+    plaslen = df.iloc[0]['qlen']
+    ticks = calc_num_markers(plaslen)
+    ticks_cds = ColumnDataSource(ticks)
+    p.multi_line(
+        xs="lineX", ys="lineY", line_color="black", line_width=2,
+        level="underlay", line_cap='round',
+        alpha=.5, source=ticks_cds)
+
+    right = ColumnDataSource(ticks[ticks['text_align'] == 'right'])
+    left = ColumnDataSource(ticks[ticks['text_align'] == 'left'])
+    bcenter = ColumnDataSource(ticks[ticks['text_align'] == 'b_center'])
+    tcenter = ColumnDataSource(ticks[ticks['text_align'] == 't_center'])
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=3, y_offset=6,
+        text_align="left", text='bp', alpha=.5,
+        text_font_size='size', level=text_level, source=right)
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=-5,
+        y_offset=6, text_align="right",
+        text='bp', alpha=.5, text_font_size='size',
+        level=text_level, source=left)
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=15,
+        text_align="center", text='bp', alpha=.5,
+        text_font_size='size', level=text_level, source=bcenter)
+    p.text(
+        x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=-3,
+        text_align="center", text='bp', alpha=.5,
+        text_font_size='size', level=text_level, source=tcenter)
+    p.add_tools(hover)
+    p.add_layout(Label(
+        x=0, y=0, name="2", x_offset=0, y_offset=-8,
+        text_align="center",
+        text=f"{plaslen} bp", text_color="#7b7b7b",
+        text_font_size='16px', level=text_level))
+    p.hover.renderers = [hover_labels]
+    p.axis.axis_label = None
+    p.axis.visible = False
+    p.grid.grid_line_color = "#EFEFEF"
+    p.outline_line_color = "#DDDDDD"
+    p.legend.location = 'bottom_left'
+    p.legend.border_line_color = "#EFEFEF"
+    p.legend.visible = True
+    return p