start adding tests for tagore, low priotiy

.gitignore

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+*.py[cod]
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+# Installer logs
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+# Unit test / coverage reports
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+.pyre/

tagore.py

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+#!/usr/bin/env python3
+'''
+tagore: a utility for illustrating human chromosomes
+https://github.com/jordanlab/tagore
+'''
+__author__ = ["Lavanya Rishishar", "Aroon Chande"]
+__copyright__ = "Copyright 2019, Applied Bioinformatics Lab"
+__license__ = "GPLv3"
+
+import os
+import pickle
+import re
+import shutil
+import subprocess
+import sys
+from argparse import ArgumentParser, HelpFormatter
+
+
+VERSION = '1.0.1'
+
+COORDINATES = {
+    "1": {"cx": 128.6, "cy": 1.5, "ht": 1654.5, "width": 118.6},
+    "2": {"cx": 301.4, "cy": 43.6, "ht": 1612.4, "width": 118.6},
+    "3": {"cx": 477.6, "cy": 341.4, "ht": 1314.7, "width": 118.6},
+    "4": {"cx": 655.6, "cy": 517.9, "ht": 1138.1, "width": 118.6},
+    "5": {"cx": 835.4, "cy": 461, "ht": 1195.1, "width": 118.6},
+    "6": {"cx": 1012.4, "cy": 524.2, "ht": 1131.8, "width": 118.6},
+    "7": {"cx": 1198.2, "cy": 608.5, "ht": 1047.5, "width": 118.6},
+    "8": {"cx": 1372.9, "cy": 692.8, "ht": 963.2, "width": 118.6},
+    "9": {"cx": 1554.5, "cy": 724.4, "ht": 931.6, "width": 118.6},
+    "10": {"cx": 1733.8, "cy": 766.6, "ht": 889.4, "width": 118.6},
+    "11": {"cx": 1911.5, "cy": 766.6, "ht": 889.4, "width": 118.6},
+    "12": {"cx": 2095.6, "cy": 769.7, "ht": 886.3, "width": 118.6},
+    "13": {"cx": 129.3, "cy": 2068.8, "ht": 766.1, "width": 118.6},
+    "14": {"cx": 301.6, "cy": 2121.5, "ht": 713.4, "width": 118.6},
+    "15": {"cx": 477.5, "cy": 2153.1, "ht": 681.8, "width": 118.6},
+    "16": {"cx": 656.7, "cy": 2232.2, "ht": 602.8, "width": 118.6},
+    "17": {"cx": 841.2, "cy": 2290.7, "ht": 544.3, "width": 118.6},
+    "18": {"cx": 1015.7, "cy": 2313.9, "ht": 521.1, "width": 118.6},
+    "19": {"cx": 1199.5, "cy": 2437.2, "ht": 397.8, "width": 118.6},
+    "20": {"cx": 1374.4, "cy": 2416.1, "ht": 418.9, "width": 118.6},
+    "21": {"cx": 1553, "cy": 2510.9, "ht": 324.1, "width": 118.6},
+    "22": {"cx": 1736.9, "cy": 2489.8, "ht": 345.1, "width": 118.6},
+    "X": {"cx": 1911, "cy": 1799.6, "ht": 1035.4, "width": 59},
+}
+
+CHROM_SIZES = {
+    "hg37": {
+        "1": 249250621, "2": 243199373, "3": 198022430, "4": 191154276,
+        "5": 180915260, "6": 171115067, "7": 159138663, "8": 146364022,
+        "9": 141213431, "10": 135534747, "11": 135006516, "12": 133851895,
+        "13": 115169878, "14": 107349540, "15": 102531392, "16": 90354753,
+        "17": 81195210, "18": 78077248, "19": 59128983, "20": 63025520,
+        "21": 48129895, "22": 51304566, "X": 155270560, "Y": 59373566
+    },
+    "hg38": {
+        "1": 248956422, "2": 242193529, "3": 198295559, "4": 190214555,
+        "5": 181538259, "6": 170805979, "7": 159345973, "8": 145138636,
+        "9": 138394717, "10": 133797422, "11": 135086622, "12": 133275309,
+        "13": 114364328, "14": 107043718, "15": 101991189, "16": 90338345,
+        "17": 83257441, "18": 80373285, "19": 58617616, "20": 64444167,
+        "21": 46709983, "22": 50818468, "X": 156040895, "Y": 57227415
+    },
+}
+
+def printif(statement, condition):
+    '''
+    Print statements if a boolean (e.g. verbose) is true
+    '''
+    if condition:
+        print(statement)
+
+def draw(arguments):
+    '''
+    Create the SVG object
+    '''
+    polygons = ""
+    try:
+        input_fh = open(arguments.input, 'r')
+    except (IOError, EOFError) as input_fh_e:
+        print("Error opening input file!")
+        raise input_fh_e
+    svg_fn = f"{arguments.prefix}.svg"
+    try:
+        svg_fh = open(svg_fn, 'w')
+        svg_fh.write(__head__)
+    except (IOError, EOFError) as svg_fh_e:
+        print("Error opening output file!")
+        raise svg_fh_e
+    line_num = 1
+    for entry in input_fh:
+        if entry.startswith("#"):
+            continue
+        entry = entry.rstrip().split("\t")
+        if len(entry) != 7:
+            print(f"Line number {line_num} does not have 7 columns")
+            sys.exit()
+        chrm, start, stop, feature, size, col, chrcopy = entry
+        chrm = chrm.replace('chr', '')
+        start = int(start)
+        stop = int(stop)
+        size = float(size)
+        feature = int(feature)
+        chrcopy = int(chrcopy)
+        if 0 > size > 1:
+            print(f"Feature size, {size},on line {line_num} unclear. \
+                Please bound the size between 0 (0%) to 1 (100%). Defaulting to 1.")
+            size = 1
+        if not re.match("^#.{6}", col):
+            print(f"Feature color, {col}, on line {line_num} unclear. \
+                Please define the color in hex starting with #. Defaulting to #000000.")
+            col = "#000000"
+        if chrcopy not in [1, 2]:
+            print(f"Feature chromosome copy, {chrcopy}, on line {line_num}\
+             unclear. Skipping...")
+            line_num = line_num + 1
+            continue
+        line_num = line_num + 1
+        if feature == 0:  # Rectangle
+            feat_start = start*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            feat_end = stop*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            width = COORDINATES[chrm]["width"]*size/2
+            if chrcopy == 1:
+                x_pos = COORDINATES[chrm]["cx"] - width
+            else:
+                x_pos = COORDINATES[chrm]["cx"]
+            y_pos = COORDINATES[chrm]["cy"] + feat_start
+            height = feat_end-feat_start
+            svg_fh.write(f"<rect x=\"{x_pos}\" y=\"{y_pos}\" fill=\"{col}\" width=\"{width}\"\
+             height=\"{height}\"/>" + "\n")
+        elif feature == 1:  # Circle
+            feat_start = start*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            feat_end = stop*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            radius = COORDINATES[chrm]["width"]*size/4
+            if chrcopy == 1:
+                x_pos = COORDINATES[chrm]["cx"] - COORDINATES[chrm]["width"]/4
+            else:
+                x_pos = COORDINATES[chrm]["cx"] + COORDINATES[chrm]["width"]/4
+            y_pos = COORDINATES[chrm]["cy"]+(feat_start+feat_end)/2
+            svg_fh.write(f"<circle fill=\"{col}\" cx=\"{x_pos}\" cy=\"{y_pos}\"\
+             r=\"{radius}\"/>" + "\n")
+        elif feature == 2:  # Triangle
+            feat_start = start*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            feat_end = stop*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            if chrcopy == 1:
+                x_pos = COORDINATES[chrm]["cx"] - COORDINATES[chrm]["width"]/2
+                sx_pos = 38.2*size
+            else:
+                x_pos = COORDINATES[chrm]["cx"] + COORDINATES[chrm]["width"]/2
+                sx_pos = -38.2*size
+            y_pos = COORDINATES[chrm]["cy"]+(feat_start+feat_end)/2
+            sy_pos = 21.5*size
+            polygons += f"<polygon fill=\"{col}\" points=\"{x_pos-sx_pos},{y_pos-sy_pos} \
+            {x_pos},{y_pos} {x_pos-sx_pos},{y_pos+sy_pos}\"/>" + "\n"
+        elif feature == 3:  # Line
+            y_pos1 = start*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            y_pos2 = stop*COORDINATES[chrm]["ht"]/CHROM_SIZES[arguments.build][chrm]
+            y_pos = (y_pos1+y_pos2)/2
+            y_pos += COORDINATES[chrm]["cy"]
+            if chrcopy == 1:
+                x_pos1 = COORDINATES[chrm]["cx"] - COORDINATES[chrm]["width"]/2
+                x_pos2 = COORDINATES[chrm]["cx"]
+                svg_fh.write(f"<line fill=\"none\" stroke=\"{col}\" stroke-miterlimit=\"10\" \
+                    x1=\"{x_pos1}\" y1=\"{y_pos}\" x2=\"{x_pos2}\" y2=\"{y_pos}\"/>" + "\n")
+            else:
+                x_pos1 = COORDINATES[chrm]["cx"]
+                x_pos2 = COORDINATES[chrm]["cx"] + COORDINATES[chrm]["width"]/2
+                svg_fh.write(f"<line fill=\"none\" stroke=\"{col}\" stroke-miterlimit=\"10\" \
+                    x1=\"{x_pos1}\" y1=\"{y_pos}\" x2=\"{x_pos2}\" y2=\"{y_pos}\"/>" + "\n")
+        else:
+            print(f"Feature type, {feature}, unclear. Please use either 0, 1, 2 or 3. Skipping...")
+            continue
+    svg_fh.write(__tail__)
+    svg_fh.write(polygons)
+    svg_fh.write("</svg>")
+    svg_fh.close()
+    printif(f"\033[92mSuccessfully created SVG\033[0m", ARGS.verbose)
+
+
+if __name__ == "__main__":
+    PARSER = ArgumentParser(prog="tagore",
+                            add_help=True,
+                            description='''
+                            tagore: a utility for illustrating human chromosomes
+                            https://github.com/jordanlab/tagore
+                            ''',
+                            formatter_class=lambda prog: HelpFormatter(prog, width=120,
+                                                                       max_help_position=120))
+
+    PARSER.add_argument('--version', action='version',
+                        help='Print the software version',
+                        version='tagore (version {})'.format(VERSION))
+
+    # Input arguments
+    PARSER.add_argument('-i', '--input', required=True, default=None, metavar='<input.bed>',
+                        help='Input BED-like file')
+    PARSER.add_argument('-p', '--prefix', required=False, default="out",
+                        metavar='[output file prefix]',
+                        help='Output prefix [Default: "out"]')
+    PARSER.add_argument('-b', '--build', required=False, default="hg38",
+                        metavar='[hg78/hg38]',
+                        help="Human genome build to use [Default: hg38]")
+    PARSER.add_argument('-f', '--force', required=False, default=False,
+                        help="Overwrite output files if they exist already",
+                        action="store_true")
+    PARSER.add_argument('-v', '--verbose', required=False, default=False,
+                        help="Display verbose output",
+                        action="store_true")
+    ARGS, UNKARGS = PARSER.parse_known_args()
+    if UNKARGS:
+        print(f"\033[93mOne or more unknown arguments were supplied:\033[0m {' '.join(UNKARGS)}\n")
+        PARSER.print_help()
+        sys.exit()
+    if ARGS.build not in ['hg37', 'hg38']:
+        print(f"\033[91mBuild must be either 'hg37' or 'hg38', you supplied {ARGS.build}.\033[0m")
+        sys.exit()
+    if shutil.which("rsvg", mode=os.X_OK) is None:
+        print(f"\033[91mCould not find `rsvg` in PATH.\033[0m")
+        sys.exit()
+    BASE_PATH = os.path.join(sys.prefix, 'lib', 'tagore-data', 'base.svg.p')
+    try:
+        BASE = open(BASE_PATH, 'rb')
+    except (IOError, EOFError) as base_e:
+        print(f"\033[91mCould not open {BASE_PATH}.  Please reinstall tagore\033[0m")
+        raise base_e
+    __head__, __tail__ = pickle.load(BASE)
+    printif(f"\033[94mDrawing chromosome ideogram using {ARGS.input}\033[0m", ARGS.verbose)
+    if os.path.exists(f"{ARGS.prefix}.svg") and ARGS.force is False:
+        print(f"\033[93m'{ARGS.prefix}.svg' already exists.\033[0m")
+        OW = input(f"Overwrite {ARGS.prefix}.svg? [Y/n]: ") or "y"
+        if OW.lower() != "y":
+            print(f"\033[93m'tagore will now exit...\033[0m")
+            sys.exit()
+        else:
+            print(f"\033[94mOverwriting existing file and saving to: {ARGS.prefix}.svg\033[0m")
+    else:
+        printif(f"\033[94mSaving to: {ARGS.prefix}.svg\033[0m", ARGS.verbose)
+    draw(ARGS)
+    printif(f"\033[94mConverting {ARGS.prefix}.svg -> {ARGS.prefix}.png\033[0m", ARGS.verbose)
+    try:
+        subprocess.check_output(f"rsvg {ARGS.prefix}.svg {ARGS.prefix}.png", shell=True)
+    except subprocess.CalledProcessError as rsvg_e:
+        printif(f"\033[91mFailed SVG to PNG conversion...\033[0m", ARGS.verbose)
+        raise rsvg_e
+    finally:
+        printif(f"\033[92mSuccessfully converted SVG to PNG\033[0m", ARGS.verbose)

tests/00_printif_test.py

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+#!/bin/env python3
+import pytest
+import sys
+from os import getcwd, path, pardir
+sys.path.append(path.abspath(path.join(getcwd())))
+from tagore import printif
+
+def test_printif_true():
+    from io import StringIO
+    output = StringIO()
+    sys.stdout = output
+    printif("Test passed", True)
+    assert output.getvalue().strip()  == "Test passed"
+
+def test_printif_false():
+    from io import StringIO
+    output = StringIO()
+    sys.stdout = output
+    printif("Test false", False)
+    assert output.getvalue().strip() == ''