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AHBrauT2
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Refinement of clustering and testing with all HQ samples done
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‎README.md

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# StraglrON
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Addon for Straglr

‎requirements.txt

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asttokens==2.4.1
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backcall==0.2.0
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biopython==1.81
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comm==0.2.0
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contourpy==1.1.1
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cycler==0.12.1
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debugpy==1.8.0
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decorator==5.1.1
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executing==2.0.1
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fonttools==4.44.0
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importlib-metadata==6.8.0
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importlib-resources==6.1.1
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ipykernel==6.26.0
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ipython==8.12.3
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jedi==0.19.1
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joblib==1.3.2
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jupyter_client==8.6.0
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jupyter_core==5.5.0
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kiwisolver==1.4.5
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matplotlib==3.7.3
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matplotlib-inline==0.1.6
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nest-asyncio==1.5.8
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numpy==1.24.4
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packaging==23.1
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pandas==2.0.3
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parso==0.8.3
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pexpect==4.8.0
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pickleshare==0.7.5
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Pillow==10.1.0
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pip==23.3
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platformdirs==4.0.0
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prompt-toolkit==3.0.40
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psutil==5.9.0
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ptyprocess==0.7.0
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pure-eval==0.2.2
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Pygments==2.16.1
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pyparsing==3.1.1
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pysam==0.22.0
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python-dateutil==2.8.2
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pytz==2023.3.post1
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pyzmq==25.1.1
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scikit-learn==1.3.2
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scipy==1.10.1
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seaborn==0.13.0
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setuptools==68.0.0
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six==1.16.0
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stack-data==0.6.3
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threadpoolctl==3.2.0
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tornado==6.3.3
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traitlets==5.13.0
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typing_extensions==4.7.1
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tzdata==2023.3
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wcwidth==0.2.5
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wheel==0.41.2
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zipp==3.11.0

‎src/.vscode/launch.json

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{
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"version": "0.2.0",
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"configurations": [
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{
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"name": "Python: Current File",
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"type": "python",
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"request": "launch",
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"program": "${file}",
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"console": "integratedTerminal",
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"args": ["/mnt/storage2/users/ahbraut2/data/snakemake_test/benchmark/straglr_test_new_Loci/og/Sample012_23014LRa.bed","--hist", "/mnt/storage2/users/ahbraut2/data/snakemake_test/benchmark/straglr_test_new_Loci/og/Sample012_23014LRa.tsv","-o", "/mnt/storage2/users/ahbraut2/scripts/TestFolder/Home", "/mnt/storage2/users/ahbraut2/data/Master_Bedfiles/RepeatLoci_straglr_LT_V2.bed" , "/mnt/storage2/users/ahbraut2/data/ONT_Pilot_TNAMSE_Links/Sample012_23014LRa.bam", "--cutoff", "5"]
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}
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]
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}

‎src/ResultGiverStraglr.py

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import os
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from collections import deque
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from pathlib import Path
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import argparse
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from utils.Structures import Expansion
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import utils.ReaderAnalyser as ra
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import utils.Visualiser as vis
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import utils.extract_repeats as extract_repeats
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import shutil
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def is_valid_file(parser, arg, type):
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"""
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Check if the provided file exists and has a .bed or .tsv extension.
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"""
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if type == "bed":
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if not os.path.exists(arg):
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parser.error(f"The file '{arg}' does not exist.")
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elif not arg.endswith('.bed'):
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parser.error(f"The file '{arg}' is not a .bed file.")
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else:
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return arg
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if type == "tsv":
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if not os.path.exists(arg):
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parser.error(f"The file '{arg}' does not exist.")
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elif not arg.endswith('.tsv'):
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parser.error(f"The file '{arg}' is not a .tsv file.")
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else:
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return arg
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#Argument parser for command line interface including necessary file and options
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parser = argparse.ArgumentParser()
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parser.add_argument("path_input_bed", type=lambda x: is_valid_file(parser, x, "bed"), help="Path to input bed file")
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parser.add_argument("path_input_tsv", type=lambda x: is_valid_file(parser, x, "tsv"), help="Path to input tsv file")
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parser.add_argument("loci_file", type=lambda x: is_valid_file(parser, x, "bed"), help="Path to Loci file used for straglr analysis")
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parser.add_argument("-o", "--output", type=str, required=True, help="Path to output folder")
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parser.add_argument("--hist", action="store_true", help="Plots histograms of pathogenic expansions")
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parser.add_argument("--score", action="store_true", help="Expansion in output file is sorted by normalized size difference score")
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parser.add_argument("--altclust", action="store_true", help="Uses Thomas Clustering")
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parser.add_argument("--alleles", action="store_true", help="Turns on the allele visualization")
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parser.add_argument("--bam", type=str, help="Location of Bam file of interest")
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parser.add_argument("-c", "--cutoff", type=int, default=2, help="Sets number of reads cutoff when clustering unimodal or bimodal allele read frequencies")
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parser.add_argument("--flank", type=int, default=25, help="flank size. Default:25")
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parser.add_argument("--genome", type=str, help="location of reference genome")
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args = parser.parse_args()
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def outputWriter(output_expansion: "list[Expansion]", sample_id, args):
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#Base output here
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sample_folder_path = args.output + "/" + sample_id
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result_file_path = sample_folder_path + "/" + sample_id + ".txt"
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if not (os.path.exists(sample_folder_path)):
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os.mkdir(sample_folder_path)
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with open(result_file_path, 'w') as f:
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print("#chr"+"\t"+"start"+"\t"+"end"+"\t"+"repeat_id"+"\t"+"repeat_unit"+"\t"+"size"+"\t"+"wt_size"+"\t"+"in_pathogenic_range"+"\t"+"size_difference"+"\t"+"allele1_support"+"\t"+"allele2_support"+"\t"+"score")
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f.write("#chr\tstart\tend\trepeat_id\trepeat_unit\tsize\twt_size\tin_pathogenic_range\tsize_difference\tallele1_support\tallele2_support\tscore\n")
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if args.altclust:
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for x in output_expansion:
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f.write(x.chr + "\t" + x.start + "\t" + x.end + "\t" + x.repeat_id + "\t" + x.repeat_unit + "\t" + str(x.allele1_size)+'/'+str(x.allele2_size) + "\t" + str(x.wt_size) + "\t" + x.in_pathogenic_range + "\t" + str(x.size_difference) + "\t" + x.allele1_support + "\t" + x.allele2_support+ "\t" + str(x.norm_score)+"\n")
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print(x.chr, x.start, x.end, x.repeat_id, x.repeat_unit, (str(x.new_allele1)+'/'+str(x.new_allele2)), x.wt_size, x.new_in_pathogenic_range, x.new_size_difference, x.new_allele1_support, x.new_allele2_support, str(x.new_norm_score))
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else:
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for x in output_expansion:
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f.write(x.chr + "\t" + x.start + "\t" + x.end + "\t" + x.repeat_id + "\t" + x.repeat_unit + "\t" + str(x.allele1_size)+'/'+str(x.allele2_size) + "\t" + str(x.wt_size) + "\t" + x.in_pathogenic_range + "\t" + str(x.size_difference) + "\t" + x.allele1_support + "\t" + x.allele2_support + "\t"+ str(x.norm_score)+"\n")
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print(x.chr, x.start, x.end, x.repeat_id, x.repeat_unit, str(x.allele1_size)+'/'+str(x.allele2_size), x.wt_size, x.in_pathogenic_range, x.size_difference, x.allele1_support, x.allele2_support, str(x.norm_score))
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#Base output plus Histograms
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if args.hist:
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plot_folder_path = sample_folder_path + "/plots"
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if(os.path.exists(plot_folder_path)):
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shutil.rmtree(plot_folder_path)
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os.mkdir(plot_folder_path)
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if args.altclust:
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for x in output_expansion:
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vis.plotHistogram(x, plot_folder_path, args.altclust)
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else:
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for x in output_expansion:
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vis.plotHistogram(x, plot_folder_path, args.altclust)
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#Base with Allele Visualization
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if args.alleles:
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repeats_fasta_folder = sample_folder_path + "/" + "repeats"
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if(os.path.exists(repeats_fasta_folder)):
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shutil.rmtree(repeats_fasta_folder)
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os.mkdir(repeats_fasta_folder)
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for x in output_expansion:
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extract_repeats.fastaMaker(args.path_input_tsv, x.chr + ":"+ x.start + "-" + x.end, args.bam, args.flank, repeats_fasta_folder + "/" + x._title + ".fa")
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vis.alleleVisualiser(repeats_fasta_folder + "/" + x._title + ".fa", x.repeat_unit, args.flank, x._title, repeats_fasta_folder, x.chr, x.start, x.end, args.genome)
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def main():
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loci_dict = ra.lociBedReader(args.loci_file)
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expansions = ra.resultBedReader(args.path_input_bed, loci_dict)
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sample_id = Path(args.path_input_bed).stem
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vis.getHistData(args.path_input_tsv, expansions)
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for expansion_object in expansions:
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if args.altclust:
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ra.newGenotyping(expansion_object, args.cutoff, False)
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ra.expansionScorer(expansion_object, args.altclust)
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if args.score:
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expansions.sort(key=lambda x: float("-Inf") if x.norm_score is None else x.norm_score, reverse=True)
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#print("score sorting working as intended")
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else:
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expansions.sort(key=lambda x: x.chr)
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#print("score sorting is turned off")
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outputWriter(expansions, sample_id, args)
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if __name__ == "__main__":
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main()

‎src/__init__.py

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‎src/__pycache__/expansion.cpython-38.pyc

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‎src/__pycache__/locus.cpython-38.pyc

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