conda

environment.yml

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+name: trackc-env
+
+dependencies:
+  - python=3.8.5
+  - matplotlib=3.6.*
+  - numpy=1.23.*
+  - pandas=1.5.*
+  - seaborn
+  - pip:
+    - cooler
+    - bioframe

src/trackc/scripts/config.yml

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+
+figure:
+  size: 
+    width: 8
+    height: 3
+
+  row: 3
+  col: 1
+
+tracks:
+  - name: M2
+    type: bw
+    gs:
+      row:
+        from: 0
+        to: 
+      col: 
+        from: 0
+        to:
+
+    pars:
+      bwfile: /annoroad/data1/bioinfo/PMO/yuanzan/RD/WDL/bw_track5/script/M2A.bw
+      chrom: chr13
+      start: 72000000
+      end: 76000000
+      color: '#464451'
+      resolution: 5000
+
+  - name: D1
+    type: bw
+    gs:
+      row:
+        from: 1
+        to: 
+      col: 
+        from: 0
+        to: 
+
+    pars:
+      bwfile: /annoroad/data1/bioinfo/PMO/yuanzan/RD/WDL/bw_track5/script/D1A.bw
+      chrom: chr13
+      start: 72000000
+      end: 76000000
+      color: '#DAD9DE'
+      resolution: 5000
+
+  - name: Blank
+    type: bw
+    gs:
+      row:
+        from: 2
+        to: 
+      col: 
+        from: 0
+        to:
+
+    pars:
+      bwfile: /annoroad/data1/bioinfo/PMO/yuanzan/RD/WDL/bw_track5/script/blankA.bw
+      chrom: chr13
+      start: 72000000
+      end: 76000000
+      color: '#E0BCC8'
+      resolution: 5000
+
+
+
+
+

src/trackc/scripts/track_view.py

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+import pandas as pd
+import numpy as np
+import os
+import sys,re
+
+import matplotlib
+import matplotlib as mpl
+mpl.rcParams['pdf.fonttype']=42
+mpl.rcParams['ps.fonttype']=42
+matplotlib.use('Agg')
+#%matplotlib inline
+
+import matplotlib.pyplot as plt
+plt.style.use('ggplot')
+import pyBigWig
+import yaml
+
+import warnings
+warnings.filterwarnings('ignore')
+
+
+def plot_bwTrack(ax, bw, ylabel, chrom, start, end, resolution=20000 , yminx=5, ymaxx=95,rotation=0, fl='%0.2f',color='#464451'):
+    ax.tick_params(bottom =False,top=False,left=True,right=False)
+    ax.spines['left'].set_color('k')
+    ax.spines['left'].set_linewidth(0.5)
+    ax.spines['bottom'].set_color('k')
+    ax.spines['bottom'].set_linewidth(0.5)
+
+    x = int((end-start)/resolution)
+
+    plot_list = bw.stats(chrom, start, end, type="mean", nBins=x)
+    plot_list = [0 if v is None else v  for v in plot_list]
+
+    width = 1
+    ax.bar(x=range(0,x), height=plot_list, width=1, bottom=[0]*(x),color=color,align="edge",edgecolor=color)    
+    ax.set_xlim(0,x)
+
+    #ax.set_xticks([])
+    #ax.set_xticklabels([])
+
+    ymin = np.percentile(plot_list,yminx)
+    ymax = np.percentile(plot_list,ymaxx)
+
+    ax.set_yticks([ymin, ymax])
+    ax.set_yticklabels([fl % ymin, fl % ymax], fontsize=7)
+
+    ax.set_ylim(ymin, ymax)
+    ax.set_ylabel(ylabel, fontsize=8, rotation=rotation, horizontalalignment='right',verticalalignment='center')
+
+    ax.set_xticks([])
+    ax.set_xticklabels('')
+
+
+def plot_bwTracks(tracks, outfile_prefix="track_test"):
+    fig = plt.figure(figsize=(int(tracks["figure"]["size"]["width"]), int(tracks["figure"]["size"]["height"])), facecolor='white')
+    plt.subplots_adjust(left=0.1, bottom=0.1, right=0.8, top=0.8, hspace=0.2, wspace=0.15)
+
+    gs = fig.add_gridspec(int(tracks["figure"]["row"]), int(tracks["figure"]["col"]))
+    ax = fig.add_subplot(gs[0, 0], facecolor='white')
+
+    for i, track in enumerate(tracks["tracks"]):
+        if track["gs"]["row"]["to"] == None:
+            if track["gs"]["col"]["to"] == None:
+                ax = fig.add_subplot(gs[int(track["gs"]["row"]["from"]), int(track["gs"]["col"]["from"])], facecolor='white')
+            else:
+                ax = fig.add_subplot(gs[int(track["gs"]["row"]["from"]), int(track["gs"]["col"]["from"]):int(track["gs"]["col"]["to"])], facecolor='white')
+        else:
+            if track["gs"]["col"]["to"] == None:
+                ax = fig.add_subplot(gs[int(track["gs"]["row"]["from"]):int(track["gs"]["row"]["to"]), int(track["gs"]["col"]["from"])], facecolor='white')
+            else:
+                ax = fig.add_subplot(gs[int(track["gs"]["row"]["from"]):int(track["gs"]["row"]["to"]), int(track["gs"]["col"]["from"]):int(track["gs"]["col"]["to"])], facecolor='white')
+
+        if track["type"] == "bw":
+            plot_bwTrack(ax, track["bwData"], track["name"], track["pars"]["chrom"], track["pars"]["start"], track["pars"]["end"], resolution=track["pars"]["resolution"], color=track["pars"]["color"])                                                                                                    
+
+    #plt.show()
+    fig.savefig(outfile_prefix + ".pdf")
+    fig.savefig(outfile_prefix + ".png")
+
+
+def get_yaml_data(yaml_file):
+    file = open(yaml_file, 'r', encoding="utf-8")
+    file_data = file.read()
+    file.close()
+
+    data = yaml.load(file_data)
+    return data
+
+def usage():
+    print("python3 track_view.py config.yml outdir outfile_prefix")
+    sys.exit(1)
+
+def main(args):
+    yml_file, outdir, outfile_prefix =  args
+    tracks = get_yaml_data(yml_file)
+
+    for i, track in enumerate(tracks["tracks"]):
+        if track["type"] == "bw":
+            tracks["tracks"][i]["bwData"] = pyBigWig.open(track["pars"]["bwfile"])
+
+    outfile_prefix = os.path.join(outdir,outfile_prefix)
+    print(outfile_prefix)
+    plot_bwTracks(tracks, outfile_prefix)
+
+
+
+if __name__ == '__main__':
+    if len(sys.argv) != 4:
+        usage()
+    main(sys.argv[1:])

src/trackc/scripts/trackc-cli.py

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+import click
+
+@click.command()
+@click.option('--regions', '-r', required=True, 
+              help="genome regions, eg.: 18:47950000-48280000 18:75280000-74850000")
+@click.option('--outfile', '-o', default='trackc.pdf',
+              help='output filename')
+def hello(regions, outfile):
+    print(1111, regions)
+    print(1111, outfile)
+
+
+if __name__ == '__main__':
+    hello()
+
+
+
+