Move graphing etc to script not core library

Author: davmlaw

bin/pyreference_biotype.py

@@ -1,19 +1,24 @@
 from __future__ import print_function, absolute_import
 
 import HTSeq
+import abc
 from argparse import ArgumentParser
 from collections import Counter
+import csv
+import logging
+from matplotlib.backends.backend_agg import FigureCanvasAgg
+from matplotlib.cm import ScalarMappable
+from matplotlib.figure import Figure
+from matplotlib.patches import Rectangle
+import os
+from pyreference import Reference
+from pyreference.utils import iv_iterators
+from pyreference.utils.file_utils import name_from_file_name, file_or_file_name
+from pyreference.utils.genomics_utils import opposite_strand, format_chrom
 import six
 import sys
 
 import numpy as np
-from pyreference import Reference
-from pyreference.utils import iv_iterators
-from pyreference.utils.csv_utils import write_csv_dict
-from pyreference.utils.file_utils import name_from_file_name
-from pyreference.utils.genomics_utils import opposite_strand, format_chrom
-from pyreference.utils.graphing import write_stacked_bar_graph, \
-    write_individual_bar_graphs
 
 
 MAX_READ_LENGTH = 200
@@ -182,6 +187,222 @@ def main():
 
 
 
+'''
+Created on 22Jan.,2018
+
+@author: dlawrence
+'''
+
+
+
+
+def axis_stacked_bar_graph(ax, largs, arrays, labels, colors):
+    bottom = np.zeros(len(largs), dtype='i')
+    for array, label, color in zip(arrays, labels, colors):
+        lines = ax.bar(largs, array, label=label, color=color, bottom=bottom, linewidth=0)
+        bottom += array
+    
+    return lines
+
+
+def write_stacked_bar_graph(graph_image, largs, arrays, labels, colors, **kwargs):
+    '''largs = x-values
+    arrays = list of lists y-values
+    labels = list of labels, same length as arrays
+    colors = list of colors, same length as arrays
+
+    kwargs:
+        extra_func = method called with args=(ax, fig, lines)
+        legend_side_ratio : eg 0.1 - Shrink figure by this
+        legend_kwargs : Passed to ax.legend
+    '''
+    logging.info("write_stacked_bar_graph: %s", graph_image)
+
+    title = kwargs.get("title")
+    extra_func = kwargs.get("extra_func")
+    subtitle = kwargs.get("subtitle")
+    x_label = kwargs.get("x_label")
+    y_label = kwargs.get("y_label")
+    legend_side_ratio = kwargs.get("legend_side_ratio")
+
+    # Old kwargs, which we passed to legend
+    legend_kwargs = {"loc" : kwargs.get("loc"),
+                     "title" : kwargs.get("legend_title"),
+                     "prop" : kwargs.get("legend_props", {})}
+    # Overwrite with legend_kwargs
+    legend_kwargs.update(kwargs.get("legend_kwargs", {}))
+
+    fig = Figure(dpi=300)
+    fig.patch.set_facecolor('white')
+    ax = fig.add_subplot(111)
+    lines = axis_stacked_bar_graph(ax, largs, arrays, labels, colors)
+
+    if title:
+        fig.suptitle(title, fontsize=18)
+    if subtitle:
+        ax.set_title(subtitle, fontsize=12)
+    if extra_func:
+        extra_func(ax, fig, lines)
+    if x_label:
+        ax.set_xlabel(x_label)
+    if y_label:
+        ax.set_ylabel(y_label)
+
+    ax.set_xlim(xmin=largs[0], xmax=largs[-1]+1)
+    
+    if legend_side_ratio is not None:
+        print("legend_side_ratio: %f" % legend_side_ratio)
+        assert 0 < legend_side_ratio < 1, "legend_side_ratio: 0 < %f < 1" % legend_side_ratio 
+        
+        # Shrink current axis's height by legend_below_ratio on the bottom
+        #ax = pyplot.axes()
+        box = ax.get_position()
+        print("Box w/h = (%f,%f)" % (box.width, box.height)) 
+        
+        new_width = box.height * (1.0 - legend_side_ratio)
+        new_position = [box.x0, box.y0,
+                        new_width, box.height]
+
+        ax.set_position(new_position)
+
+        box = ax.get_position()
+        print("NEW Box w/h = (%f,%f)" % (box.width, box.height)) 
+
+
+    print("**legend_kwargs = %s" % legend_kwargs)
+    ax.legend(**legend_kwargs)
+    
+    canvas = FigureCanvasAgg(fig)
+    canvas.print_png(graph_image)
+
+def write_individual_bar_graphs(graph_image, largs, arrays, labels, colors, **kwargs):
+    ''' same as write_stacked_bar_graph but writes out 1 plot per entry in array '''
+
+    (name_base, extension) = os.path.splitext(graph_image)
+    
+    title = kwargs.get("title", "")
+    y_label = kwargs.get("y_label", None)
+    for array, label, color in zip(arrays, labels, colors):
+        kwargs["title"] = "%s (%s)" % (title, label)
+        kwargs["color"] = color
+
+        bargraph = BarGraph(largs, array)
+        bargraph.y_label = y_label
+        individual_graph_image = "%s.%s%s" % (name_base, label, extension) # extension still has dot
+        bargraph.save(individual_graph_image)
+    
+    
+class GraphBase(object):
+    __metaclass__ = abc.ABCMeta
+
+    def __init__(self, **kwargs):
+        '''
+            legend: [('label', 'color'), ('label2', 'color2')]
+        '''
+        self.title = kwargs.get("title")
+        self.x_label = kwargs.get("x_label")
+        self.y_label = kwargs.get("y_label")
+        self.legend = kwargs.get('legend')
+        self.plot_methods = [self.plot]
+
+    def decorations(self, ax):
+        if self.title:
+            ax.set_title(self.title)
+        if self.x_label:
+            ax.set_xlabel(self.x_label)
+        if self.y_label:
+            ax.set_ylabel(self.y_label)
+
+    @abc.abstractmethod
+    def plot(self, ax):
+        return
+
+    def post_plot(self, ax):
+        if self.legend:
+            patches = []
+            labels = []
+            for (name, color) in self.legend:
+                labels.append(name)
+                patches.append(Rectangle((0, 0), 1, 1, fc=color))
+
+            ax.legend(patches, labels, loc='upper left')
+
+    def figure(self, figure):
+        ''' a hook method if you want to do something about the figure '''
+        pass
+
+    def get_figure_and_axis(self, dpi):
+        figure = Figure(dpi=dpi)
+        figure.patch.set_facecolor('white')
+        ax = figure.add_subplot(1, 1, 1)
+        return figure, ax
+
+    def save(self, filename_or_obj, dpi=None, file_type='png'):
+        figure, ax = self.get_figure_and_axis(dpi)
+        
+        self.decorations(ax)
+        for plot in self.plot_methods:
+            plot(ax) # Implementation
+        self.post_plot(ax)
+        self.figure(figure)
+
+        canvas = FigureCanvasAgg(figure)
+        if file_type == 'png':
+            canvas.print_png(filename_or_obj)
+        elif file_type == 'pdf':
+            canvas.print_pdf(filename_or_obj)
+        
+    def draw_origin(self, ax):
+        ax.axvline(c='black', lw=0.5) 
+        ax.axhline(c='black', lw=0.5)
+
+    def colorbar_from_cmap_array(self, figure, cmap, array):        
+        mappable = ScalarMappable(cmap=cmap)
+        mappable.set_array(array)
+        figure.colorbar(mappable)
+    
+
+def write_csv_dict(csv_file, headers, rows, extrasaction=None, dialect=None):
+    '''
+    default dialect = 'excel', other dialect option: 'excel-tab'
+    These are the same optional arguments as csv.DictWriter
+    headers=keys for dicts
+    rows=list of dicts
+    '''
+
+    
+    if extrasaction is None:
+        extrasaction = "raise"
+    if dialect is None:
+        dialect = 'excel'
+    
+    f = file_or_file_name(csv_file, "wb")
+
+    writer = csv.DictWriter(f, headers, extrasaction=extrasaction, dialect=dialect)
+    writer.writerow(dict(zip(headers, headers)))
+    writer.writerows(rows)
+
+    
+    
+class BarGraph(GraphBase):
+    def __init__(self, x, y, **kwargs):
+        super(BarGraph, self).__init__(**kwargs)
+        self.x = x
+        self.y = y
+        self.labels = kwargs.get("labels")
+        self.color = kwargs.get("color")
+        
+    def plot(self, ax):
+        width = 0.5
+
+        ax.set_xlim(xmin=self.x[0], xmax=self.x[-1]+1)
+        ax.bar(self.x, self.y, width=width, color=self.color)
+
+        if self.labels:
+            ax.set_xticks(self.x + width/2)
+            ax.set_xticklabels(self.labels)
+
+
 
 if __name__ == '__main__':
     main()

bin/gtf_to_json.py bin/pyreference_gtf_to_json.pybin/gtf_to_json.py renamed to bin/pyreference_gtf_to_json.py

@@ -1,16 +1,16 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 from __future__ import print_function, absolute_import
 
 import HTSeq
 from collections import defaultdict
 import gzip
 import json
-import sys
-
+import os
 from pyreference.settings import CHROM, START, END, STRAND, IS_CODING, CODING_FEATURES, \
     PYREFERENCE_JSON_VERSION_KEY, PYREFERENCE_JSON_VERSION
 from pyreference.utils.file_utils import name_from_file_name
+import sys
 
 
 class SetEncoder(json.JSONEncoder):
@@ -75,7 +75,8 @@ def add_UTR_features(transcripts_by_id, transcript_cds_by_id):
 
 def main():
     if len(sys.argv) != 2:
-        print(sys.stderr, "Usage: %s reference.gtf" % sys.argv[0])
+        script_name = os.path.basename(__file__)
+        print("Usage: %s reference.gtf" % script_name, file=sys.stderr)
         sys.exit(1)
 
     gtf_file = sys.argv[1]

bin/test_reference.py

@@ -1,7 +1,9 @@
 from __future__ import absolute_import
 
-from .transcript import *
 from .gene import *
+from .mirna import *
 from .reference import *
+from .referenceargparse import *
+from .transcript import *
 
 

pyreference/__init__.py

@@ -1,15 +1,11 @@
 '''
-Created on 23Jan.,2018
 
-@author: dlawrence
-'''
+ACRF Cancer Genomics Facility
 
-'''
+Created on 23Jan.,2018
 
 @see http://www.mirbase.org/
 
-Created on Sep 6, 2012
-
 @author: dlawrence
 '''