Move scripts

HiFi-MAG-Pipeline/scripts/Checkm-Plot.py

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+import argparse
+import pandas as pd
+import seaborn as sns
+import matplotlib.pyplot as plt
+
+
+def get_args():
+    """
+    Get arguments from command line with argparse.
+    """
+    parser = argparse.ArgumentParser(
+        prog='Metabat-Plot.py',
+        description="""Plot bin information from MetaBAT2.""")
+
+    parser.add_argument("-i", "--input",
+                        required=True,
+                        help="The o2 format summary file from CheckM.")
+    parser.add_argument("-l", "--label",
+                        required=True,
+                        help="A label for the plot.")
+    parser.add_argument("-c", "--completeness",
+                        required=True,
+                        type=int,
+                        help="Completeness threshold.")
+    parser.add_argument("-m", "--contamination",
+                        required=True,
+                        type=int,
+                        help="Contamination threshold.")
+    parser.add_argument("-g", "--contigs",
+                        required=True,
+                        type=int,
+                        help="Contigs threshold.")
+    parser.add_argument("-o1", "--output1",
+                        required=True,
+                        help="The name of the output file (a plot).")
+    parser.add_argument("-o2", "--output2",
+                        required=True,
+                        help="The name of the output file (a plot).")
+    parser.add_argument("-o3", "--output3",
+                        required=True,
+                        help="The name of the output file (a plot).")
+    parser.add_argument("-o4", "--output4",
+                        required=True,
+                        help="The name of the output file (a plot).")
+    parser.add_argument("-o5", "--output5",
+                        required=True,
+                        help="The name of the output file (a plot).")
+    parser.add_argument("-o6", "--output6",
+                        required=True,
+                        help="The name of the output file (a plot).")
+
+    return parser.parse_args()
+
+
+def create_unfiltered_joint_scatter(df, output):
+    sns.jointplot(data=df, x='Completeness', y='Contamination', s=50, alpha=0.7, xlim=(-2,102), ylim=(-2,102))
+    plt.savefig("{}".format(output))
+    plt.close()
+
+def create_unfiltered_scatter_bins(df, label, output, completeness, contamination):
+    ax = df.plot.scatter(x='Completeness', y='Contamination', s=40, alpha=0.9, xlim=(-2,102), ylim=(-2,102))
+    for i, txt in enumerate(df['Bin Id']):
+        ax.annotate(txt, (df['Completeness'].iat[i], df['Contamination'].iat[i]),
+                    xytext=(df['Completeness'].iat[i] + 0.15, df['Contamination'].iat[i] + 0.15),
+                    fontsize=5)
+    plt.xlabel('Genome Completeness')
+    plt.ylabel('Genome Contamination')
+    plt.title("Unfiltered Genome Bins: {}\n(labeled by bin name)".format(label))
+    plt.savefig("{}".format(output))
+    plt.close()
+
+def create_unfiltered_scatter_contigs(df, label, output, completeness, contamination):
+    ax = df.plot.scatter(x='Completeness', y='Contamination', s=40, alpha=0.9, xlim=(-2,102), ylim=(-2,102))
+    for i, txt in enumerate(df['# contigs']):
+        ax.annotate(txt, (df['Completeness'].iat[i], df['Contamination'].iat[i]),
+                    xytext=(df['Completeness'].iat[i] + 0.15, df['Contamination'].iat[i] + 0.15),
+                    fontsize=5)
+    plt.xlabel('Genome Completeness')
+    plt.ylabel('Genome Contamination')
+    plt.title("Unfiltered Genome Bins: {}\n(labeled with numbers of contigs in bins)".format(label))
+    plt.savefig("{}".format(output))
+    plt.close()
+
+def create_filtered_scatter(df, label, output, completeness, contamination):
+    ax = df.plot.scatter(x='Completeness', y='Contamination', s=40, alpha=0.9, xlim=((completeness-2),102), ylim=(-0.5,(contamination+0.5)))
+    plt.xlabel('Genome Completeness')
+    plt.ylabel('Genome Contamination')
+    plt.title("Filtered Genome Bins: {}".format(label))
+    plt.savefig("{}".format(output))
+    plt.close()
+
+def create_filtered_scatter_contigs(df, label, output, completeness, contamination):
+    ax = df.plot.scatter(x='Completeness', y='Contamination', s=40, alpha=0.9, xlim=((completeness-2),102), ylim=(-0.5,(contamination+0.5)))
+    for i, txt in enumerate(df['# contigs']):
+        ax.annotate(txt, (df['Completeness'].iat[i], df['Contamination'].iat[i]),
+                    xytext=(df['Completeness'].iat[i] + 0.1, df['Contamination'].iat[i] + 0.15),
+                    fontsize=6)
+    plt.xlabel('Genome Completeness')
+    plt.ylabel('Genome Contamination')
+    plt.title("Filtered Genome Bins: {}\n(labeled with numbers of contigs in bins)".format(label))
+    plt.savefig("{}".format(output))
+    plt.close()
+
+def create_filtered_scatter_bins(df, label, output, completeness, contamination):
+    ax = df.plot.scatter(x='Completeness', y='Contamination', s=40, alpha=0.9, xlim=((completeness-2),102), ylim=(-0.5,(contamination+0.5)))
+    for i, txt in enumerate(df['Bin Id']):
+        ax.annotate(txt, (df['Completeness'].iat[i], df['Contamination'].iat[i]),
+                    xytext=(df['Completeness'].iat[i] + 0.1, df['Contamination'].iat[i] + 0.12),
+                    fontsize=5)
+    plt.xlabel('Genome Completeness')
+    plt.ylabel('Genome Contamination')
+    plt.title("Filtered Genome Bins: {}\n(labeled by bin name)".format(label))
+    plt.savefig("{}".format(output))
+    plt.close()
+
+
+def main():
+    args = get_args()
+    df = pd.read_csv(args.input, sep='\t')
+    scatfilt = (df['Completeness'] >= args.completeness) & (df['Contamination'] <= args.contamination) & (df['# contigs'] < args.contigs)
+    filt = df[scatfilt]
+    create_unfiltered_joint_scatter(df, args.output1, args.completeness, args.contamination)
+    create_unfiltered_scatter_contigs(df, args.label, args.output2, args.completeness, args.contamination)
+    create_unfiltered_scatter_bins(df, args.label, args.output3, args.completeness, args.contamination)
+    create_filtered_scatter(filt, args.label, args.output4, args.completeness, args.contamination)
+    create_filtered_scatter_contigs(filt, args.label, args.output5, args.completeness, args.contamination)
+    create_filtered_scatter_bins(filt, args.label, args.output6, args.completeness, args.contamination)
+
+if __name__ == '__main__':
+    main()
+

HiFi-MAG-Pipeline/scripts/Concoct-organize-outputs.py

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+import argparse
+import os
+import shutil
+
+def get_args():
+    """
+    Get arguments from command line with argparse.
+    """
+    parser = argparse.ArgumentParser(
+        prog='Concoct-organize-outputs.py',
+        description="""Relabel bin files from concoct.""")
+    parser.add_argument("-i", "--indir",
+                        required=True,
+                        help="Name of output directory.")
+    return parser.parse_args()
+
+def relabel_outputs(indir):
+    os.chdir(indir)
+    fasta_files = [f for f in os.listdir('.') if f.endswith('.fa')]
+    for f in fasta_files:
+        outname = "concoct.{}.{}".format(f.split('.')[0], f.split('.')[-1])
+        print("Relabeling file: {}".format(f))
+        print("\t{}".format(outname))
+        shutil.move(f, os.path.join(indir, outname))
+
+def main():
+    args = get_args()
+    relabel_outputs(args.indir)
+    print("Finished.")
+
+if __name__ == '__main__':
+    main()

HiFi-MAG-Pipeline/scripts/Make-maxbin-depths.py

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+import argparse
+import os
+
+def get_args():
+    """
+    Get arguments from command line with argparse.
+    """
+    parser = argparse.ArgumentParser(
+        prog='Make-maxbin-depths.py',
+        description="""Filter JGI depths for maxbin.""")
+
+    parser.add_argument("-i", "--infile",
+                        required=True,
+                        help="Path to JGI depth file.")
+    parser.add_argument("-o", "--outfile",
+                        required=True,
+                        help="Name of output depth file.")
+    return parser.parse_args()
+
+def write_new_depth_file(input_depth_file, output_depth_file):
+    """
+    contigName      contigLen       totalAvgDepth   sludge.bam      sludge.bam-var
+    s0.ctg000001c   4.13709e+06     61.7612 61.7612 103.936
+    s1.ctg000002c   2.23849e+06     14.3086 14.3086 33.5774
+    s2.ctg000003l   40246   10.6046 10.6046 38.4902
+    s3.ctg000004l   461151  4.44724 4.44724 3.09768
+    s4.ctg000005l   516089  30.5501 30.5501 65.15
+    s5.ctg000006l   1.6986e+06      8.46604 8.46604 13.8984
+    s2.ctg000007l   24711   0.643378        0.643378        0.229328
+    s6.ctg000008l   31810   35.0132 35.0132 468.885
+    s7.ctg000009c   3.24454e+06     200.377 200.377 1599.71
+    """
+    if os.path.exists(output_depth_file):
+        print("Removing existing version of file.")
+        os.remove(output_depth_file)
+
+    with open(input_depth_file, 'r') as fh_in, open(output_depth_file, 'a') as fh_out:
+        kept_count = int(0)
+        for line in fh_in:
+            if line.startswith("contigName"):
+                pass
+            else:
+                fh_out.write("{}\t{}\n".format(line.split('\t')[0], line.split('\t')[2]))
+                kept_count += 1
+        print("Parsed {:,} contigs".format(kept_count))
+
+def main():
+    args = get_args()
+    write_new_depth_file(args.infile, args.outfile)
+
+if __name__ == '__main__':
+    main()
+

HiFi-MAG-Pipeline/scripts/Maxbin2-organize-outputs.py

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+import argparse
+import os
+import shutil
+
+def get_args():
+    """
+    Get arguments from command line with argparse.
+    """
+    parser = argparse.ArgumentParser(
+        prog='Maxbin2-organize-outputs.py',
+        description="""Organize output files from maxbin2.""")
+    parser.add_argument("-s", "--sample",
+                        required=True,
+                        help="The sample name.")
+    parser.add_argument("-o", "--outdir",
+                        required=True,
+                        help="Name of output directory.")
+    return parser.parse_args()
+
+def make_outdir(outdir):
+    fulldir = os.path.join(os.getcwd(), outdir)
+    if not os.path.exists(fulldir):
+        os.mkdir(fulldir)
+    print("Created directory: {}".format(fulldir))
+    return fulldir
+
+def move_outputs(sample, fulldir):
+    target_files = [f for f in os.listdir('.') if f.startswith(sample)
+                    and f.endswith(('.seed', '.log', '.marker', '.tar.gz', '.noclass', '.summary', '.tooshort'))]
+    for f in target_files:
+        print("\tMoving file: {}".format(f))
+        shutil.move(f, fulldir)
+
+    fasta_files = [f for f in os.listdir('.') if f.startswith(sample)
+                    and f.endswith('.fasta')]
+    for f in fasta_files:
+        outname = "maxbin.{}.{}".format(f.split('.')[1], f.split('.')[-1])
+        print("Relabeling file: {}".format(f))
+        print("\t{}".format(outname))
+        shutil.move(f, os.path.join(fulldir, outname))
+
+def main():
+    args = get_args()
+    fulldir = make_outdir(args.outdir)
+    move_outputs(args.sample, fulldir)
+    print("Finished.")
+
+if __name__ == '__main__':
+    main()