image_analyzer.py

import os
import argparse
from PIL import Image, ImageOps
import numpy as np
import math


def get_base_by_color(base):
    """
    Get color based on a base.
    - Uses different band of the same channel.
    :param base:
    :return:
    """
    if base >= 250.0:
        return 'A'
    if base >= 180.0:
        return 'G'
    if base >= 100.0:
        return 'C'
    if base >= 30.0:
        return 'T'
    if base >= 5.0:
        return '*'


def get_alt_support_by_color(is_in_support):
    """
    ***NOT USED YET***
    :param is_in_support:
    :return:
    """
    if is_in_support == 254.0:
        return 1
    elif is_in_support == 152.0:
        return 0


def get_quality_by_color(map_quality):
    """
    Get a color spectrum given mapping quality
    :param map_quality: value of mapping quality
    :return:
    """
    color = math.floor(((map_quality / 254) * 9))
    return color

def get_match_ref_color(is_match):
    """
    Get color for base matching to reference
    :param is_match: If true, base matches to reference
    :return:
    """
    if is_match == 50:
        return 1
    elif is_match == 254:
        return 0


def get_strand_color(is_rev):
    """
    Get color for forward and reverse reads
    :param is_rev: True if read is reversed
    :return:
    """
    if is_rev == 240.0:
        return 1
    else:
        return 0


def get_cigar_by_color(cigar_code):
    """
    ***NOT USED YET***
    :param is_in_support:
    :return:
    """
    if cigar_code == 254:
        return 0
    if cigar_code == 152:
        return 1
    if cigar_code == 76:
        return 2


def analyze_it(img):
    file = img
    img = Image.open(file)

    shape = (300, 300, 7)
    np_array_of_img = np.array(img.getdata())

    img = np.reshape(np_array_of_img, shape)
    img = np.transpose(img, (0, 1, 2))
    print("BASE CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[i][j][0] != 0:
                print(get_base_by_color(img[i][j][0]), end='')
            else:
                print(' ',end='')
        print()
    print("CIGAR CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[i][j][6] != 0:
                print(get_cigar_by_color(img[i][j][6]), end='')
            else:
                print(' ', end='')
        print()
    print("SUPPORT CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[i][j][5] != 0:
                print(get_alt_support_by_color(img[i][j][5]), end='')
            else:
                print(' ', end='')
        print()

    print("BASE QULAITY CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[i][j][1] != 0:
                print(get_quality_by_color(img[i][j][1]), end='')
            else:
                print(' ', end='')
        print()

    print("MAP QUALITY CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[i][j][2] != 0:
                print(get_quality_by_color(img[i][j][2]), end='')
            else:
                print(' ', end='')
        print()

    print("MISMATCH CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[i][j][4] != 0:
                print(get_match_ref_color(img[i][j][4]), end='')
            else:
                print(' ', end='')
        print()

    print("STRAND CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[i][j][3] != 0:
                print(get_strand_color(img[i][j][3]), end='')
            else:
                print(' ', end='')
        print()


def analyze_np_array(img):
    img = img.numpy() * 255
    # img = np.reshape(np_array_of_img, shape)
    # img = np.transpose(img, (0, 1, 2))
    print("BASE CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[0][i][j] != 0:
                print(get_base_by_color(img[0][i][j]), end='')
            else:
                print(' ',end='')
        print()

    print("CIGAR CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[6][i][j] != 0:
                print(get_cigar_by_color(img[6][i][j]), end='')
            else:
                print(' ', end='')
        print()
    print("SUPPORT CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[5][i][j] != 0:
                print(get_alt_support_by_color(img[5][i][j]), end='')
            else:
                print(' ', end='')
        print()

    print("BASE QULAITY CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[1][i][j] != 0:
                print(get_quality_by_color(img[1][i][j]), end='')
            else:
                print(' ', end='')
        print()

    print("MAP QUALITY CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[2][i][j] != 0:
                print(get_quality_by_color(img[2][i][j]), end='')
            else:
                print(' ', end='')
        print()

    print("MISMATCH CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[4][i][j] != 0:
                print(get_match_ref_color(img[4][i][j]), end='')
            else:
                print(' ', end='')
        print()

    print("STRAND CHANNEL")
    for i in range(300):
        for j in range(300):
            if img[3][i][j] != 0:
                print(get_strand_color(img[3][i][j]), end='')
            else:
                print(' ', end='')
        print()

if __name__ == '__main__':
    """
    Processes arguments and performs tasks to generate the pileup.
    """

    parser = argparse.ArgumentParser()
    parser.register("type", "bool", lambda v: v.lower() == "true")
    parser.add_argument(
        "--img",
        type=str,
        required=True,
        help="Path to the image."
    )
    FLAGS, not_parsed_flags = parser.parse_known_args()
    # make output directory if not already created
    analyze_it(FLAGS.img)