# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
#

"""Example of using GenomeDiagram cross-links to mimic ACT."""

from __future__ import print_function

import sys
import os
from reportlab.lib import colors
from reportlab.lib.units import cm

from Bio.Graphics.GenomeDiagram import Diagram, CrossLink
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio import SeqIO

# Modify this line to point at the Artemis/ACT example data which is online at:
# https://github.com/sanger-pathogens/Artemis/tree/master/etc
input_folder = "/Applications/Artemis/Artemis.app/Contents/artemis/etc"

name = "af063097_v_b132222"
file_a = "af063097.embl"
file_b = "b132222.embl"
format_a = "embl"
format_b = "embl"
file_a_vs_b = "af063097_v_b132222.crunch"

for f in [file_a, file_b, file_a_vs_b]:
    if not os.path.isfile(os.path.join(input_folder, f)):
        print("Missing input file %s.fna" % f)
        sys.exit(1)

# Only doing a_vs_b here, could also have b_vs_c and c_vs_d etc
genomes = [
    (os.path.join(input_folder, file_a), format_a),
    (os.path.join(input_folder, file_b), format_b),
]
comparisons = [os.path.join(input_folder, file_a_vs_b)]

# Create diagram with tracks, each with a feature set
assert len(genomes) >= 2 and len(genomes) == len(comparisons) + 1
gd_diagram = Diagram(name, track_size=0.35, circular=False)
tracks = {}
feature_sets = {}
records = {}
for f, format in genomes:
    records[f] = SeqIO.read(f, format)
    tracks[f] = gd_diagram.new_track(1, name=f, start=0, end=len(records[f]),
                                     scale_smalltick_interval=1000,
                                     scale_largetick_interval=10000,
                                     greytrack=True, greytrack_labels=0)
    feature_sets[f] = tracks[f].new_set()

print("Drawing matches...")
for i, crunch_file in enumerate(comparisons):
    q = genomes[i + 1][0]  # query file
    s = genomes[i][0]  # subject file
    q_set = feature_sets[q]
    s_set = feature_sets[s]
    with open(crunch_file) as handle:
        for line in handle:
            if line[0] == "#":
                continue
            parts = line.rstrip("\n").split(None, 7)
            # 0 = score
            # 1 = id
            # 2 = S1
            # 3 = E1
            # 4 = seq1
            # 5 = S2
            # 6 = E2
            # 7 = seq2
            try:
                q_start, q_end = int(parts[2]), int(parts[3])
                s_start, s_end = int(parts[5]), int(parts[6])
            except IndexError:
                sys.stderr.write(repr(line) + "\n")
                sys.stderr.write(repr(parts) + "\n")
                raise
            flip = False
            if q_start > q_end:
                flip = not flip
                q_start, q_end = q_end, q_start
            if s_start > s_end:
                flip = not flip
                s_start, s_end = s_end, s_start
            if flip:
                c = colors.Color(0, 0, 1, alpha=0.25)
                b = False
            else:
                c = colors.Color(1, 0, 0, alpha=0.25)
                b = False
            q_feature = q_set.add_feature(SeqFeature(FeatureLocation(q_start - 1, q_end)),
                                          color=c, border=b)
            s_feature = s_set.add_feature(SeqFeature(FeatureLocation(s_start - 1, s_end)),
                                          color=c, border=b)
            gd_diagram.cross_track_links.append(CrossLink(q_feature, s_feature, c, b))
            # NOTE: We are using the same colour for all the matches,
            # with transparency. This means overlayed matches will appear darker.
            # It also means the drawing order not very important.
            # Note ACT puts long hits at the back, and colours by hit score

print("Drawing CDS features...")
for f, format in genomes:
    record = records[f]
    feature_set = feature_sets[f]
    # Mark the CDS features
    for cds in record.features:
        if cds.type != "CDS":
            continue
        feature_set.add_feature(cds, sigil="ARROW",
                                color=colors.lightblue,
                                border=colors.blue)

gd_diagram.draw(format="linear", fragments=3,
                orientation="landscape", pagesize=(20 * cm, 10 * cm))
gd_diagram.write(name + ".pdf", "PDF")

gd_diagram.draw(format="circular",
                orientation="landscape", pagesize=(20 * cm, 20 * cm))
gd_diagram.write(name + "_c.pdf", "PDF")
