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%load_ext autoreload
%autoreload 2
%matplotlib inline

from argparse import Namespace
import misc.logging_utils as logging_utils

args = Namespace()
logger = logging_utils.get_ipython_logger()


    

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import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns; sns.set(style='white')

import misc.bio_utils.bed_utils as bed_utils
import misc.mpl_utils as mpl_utils
import riboutils.ribo_utils as ribo_utils


    

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args.orfs = "/path/to/my/filtered.predicted-orfs.bed.gz"
args.out = "/path/to/my/filtered.predicted-orfs.bar-chart.pdf"
args.use_groups = False
args.title = "My Title"


    

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def get_orf_label_counts(counts, orf_label):
    orf_types = ribo_utils.orf_type_labels_mapping[orf_label]
    orf_label_counts = np.sum(counts[orf_types])
    
    if np.isnan(orf_label_counts):
        orf_label_counts = 0
    return orf_label_counts


    

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orfs = bed_utils.read_bed(args.orfs)

strands = ['+', '-']
fracs = []
labels = []
for strand in ['+', '-']:
    m_strand = orfs['strand'] == strand
    orf_type_groups = orfs[m_strand].groupby('orf_type')
    counts = orf_type_groups.size()

    if args.use_groups:
        lab = ribo_utils.orf_type_labels
        fr = [get_orf_label_counts(counts, l) for l in lab]
    else:
        fr = counts.values
        lab = np.array(counts.index)

    lab = ["{} ({})".format(l,f) for l,f in zip(lab, fr)]

    fracs.append(fr)
    labels.append(lab)

fig, axes = plt.subplots(ncols=2, figsize=(10,5))

cmap = plt.cm.Blues
colors = cmap(np.linspace(0., 1., len(labels[0])))

# forward strand ORFs

extra_artists = []
if sum(fracs[0]) > 0:
    patches, texts = axes[0].pie(fracs[0], colors=colors)
    lgd = axes[0].legend(patches, labels[0], loc="center right", bbox_to_anchor=(0,0.5))
    axes[0].set_title("Strand: {}".format(strands[0]))

    extra_artists.append(lgd)
else:
    title = "Strand: {}. No ORFs".format(strands[0])
    axes[0].set_title(title)
    axes[0].set_axis_off()

# reverse strand ORFs
if sum(fracs[1]) > 0:
    patches, texts = axes[1].pie(fracs[1], colors=colors)
    lgd = axes[1].legend(patches, labels[1], loc="center right", bbox_to_anchor=(2.0,0.5))
    axes[1].set_title("Strand: {}".format(strands[1]))
    extra_artists.append(lgd)
else:
    title = "Strand: {}. No ORFs".format(strands[1])
    axes[1].set_title(title)
    axes[1].set_axis_off()

if (args.title is not None) and (len(args.title) > 0):
    sup = fig.suptitle(args.title)
    extra_artists.append(sup)

if args.out is not None:
    fig.savefig(args.out, bbox_extra_artists=extra_artists, bbox_inches='tight')