kkonganti@1: #!/usr/bin/env python3
kkonganti@1: 
kkonganti@1: # Kranti Konganti
kkonganti@1: 
kkonganti@1: import argparse
kkonganti@1: import glob
kkonganti@1: import inspect
kkonganti@1: import json
kkonganti@1: import logging
kkonganti@1: import os
kkonganti@1: import pickle
kkonganti@1: import pprint
kkonganti@1: import re
kkonganti@1: from collections import defaultdict
kkonganti@1: 
kkonganti@1: import yaml
kkonganti@1: 
kkonganti@1: 
kkonganti@1: # Multiple inheritence for pretty printing of help text.
kkonganti@1: class MultiArgFormatClasses(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
kkonganti@1:     pass
kkonganti@1: 
kkonganti@1: 
kkonganti@1: # Main
kkonganti@1: def main() -> None:
kkonganti@1:     """
kkonganti@1:     The succesful execution of this script requires access to bettercallsal formatted
kkonganti@1:     db flat files. On raven2, they are at /hpc/db/bettercallsall/PDGXXXXXXXXXX.XXXXX
kkonganti@1: 
kkonganti@1:     It takes the ACC2SERO.pickle file and *.reference_target.cluster_list.tsv file
kkonganti@1:     for that particular NCBI Pathogens release from the db directory mentioned with
kkonganti@1:     -db option and a root parent directory of the `salmon quant` results mentioned
kkonganti@1:     with -sal option and generates a final results table with number of reads
kkonganti@1:     mapped and a .json file to be used with MultiQC to generate a stacked bar plot.
kkonganti@1: 
kkonganti@1:     Using -url option optionally adds an extra column of NCBI Pathogens Isolates
kkonganti@1:     Browser, which directly links out to NCBI Pathogens Isolates SNP viewer tool.
kkonganti@1:     """
kkonganti@1:     # Set logging.
kkonganti@1:     logging.basicConfig(
kkonganti@1:         format="\n" + "=" * 55 + "\n%(asctime)s - %(levelname)s\n" + "=" * 55 + "\n%(message)s\n\n",
kkonganti@1:         level=logging.DEBUG,
kkonganti@1:     )
kkonganti@1: 
kkonganti@1:     # Debug print.
kkonganti@1:     ppp = pprint.PrettyPrinter(width=55)
kkonganti@1:     prog_name = inspect.stack()[0].filename
kkonganti@1: 
kkonganti@1:     parser = argparse.ArgumentParser(
kkonganti@1:         prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
kkonganti@1:     )
kkonganti@1: 
kkonganti@1:     required = parser.add_argument_group("required arguments")
kkonganti@1: 
kkonganti@1:     required.add_argument(
kkonganti@1:         "-sal",
kkonganti@1:         dest="salmon_res_dir",
kkonganti@1:         default=False,
kkonganti@1:         required=True,
kkonganti@1:         help="Absolute UNIX path to the parent directory that contains the\n"
kkonganti@1:         + "`salmon quant` results directory. For example, if path to\n"
kkonganti@1:         + "`quant.sf` is in /hpc/john_doe/test/salmon_res/quant.sf, then\n"
kkonganti@1:         + "use this command-line option as:\n"
kkonganti@1:         + "-sal /hpc/john_doe/test",
kkonganti@1:     )
kkonganti@1:     required.add_argument(
kkonganti@1:         "-snp",
kkonganti@1:         dest="rtc",
kkonganti@1:         default=False,
kkonganti@1:         required=True,
kkonganti@1:         help="Absolute UNIX Path to the PDG SNP reference target cluster\n"
kkonganti@1:         + "metadata file. On raven2, these are located at\n"
kkonganti@1:         + "/hpc/db/bettercallsal/PDGXXXXXXXXXX.XXXXX\n"
kkonganti@1:         + "Required if -sal is on.",
kkonganti@1:     )
kkonganti@1:     required.add_argument(
kkonganti@1:         "-pickle",
kkonganti@1:         dest="acc2sero",
kkonganti@1:         default=False,
kkonganti@1:         required=True,
kkonganti@1:         help="Absolute UNIX Path to the *ACC2SERO.pickle\n"
kkonganti@1:         + "metadata file. On raven2, these are located at\n"
kkonganti@1:         + "/hpc/db/bettercallsal/PDGXXXXXXXXXX.XXXXX\n"
kkonganti@1:         + "Required if -sal is on.",
kkonganti@1:     )
kkonganti@1:     parser.add_argument(
kkonganti@1:         "-op",
kkonganti@1:         dest="out_prefix",
kkonganti@1:         default="bettercallsal.tblsum",
kkonganti@1:         required=False,
kkonganti@1:         help="Set the output file(s) prefix for output(s) generated\n" + "by this program.",
kkonganti@1:     )
kkonganti@1:     parser.add_argument(
kkonganti@1:         "-url",
kkonganti@1:         dest="show_snp_clust_info",
kkonganti@1:         default=False,
kkonganti@1:         required=False,
kkonganti@1:         action="store_true",
kkonganti@1:         help="Show SNP cluster participation information of the final genome hit.\n"
kkonganti@1:         + "This may be useful to see a relative placement of your sample in\n"
kkonganti@1:         + "NCBI Isolates SNP Tree Viewer based on genome similarity but however\n"
kkonganti@1:         + "due to rapid nature of the updates at NCBI Pathogen Detection Project,\n"
kkonganti@1:         + "the placement may be in an outdated cluster.",
kkonganti@1:     )
kkonganti@1: 
kkonganti@1:     args = parser.parse_args()
kkonganti@1:     salmon_res_dir = args.salmon_res_dir
kkonganti@1:     out_prefix = args.out_prefix
kkonganti@1:     show_snp_clust_col = args.show_snp_clust_info
kkonganti@1:     rtc = args.rtc
kkonganti@1:     pickled_sero = args.acc2sero
kkonganti@1:     no_hit = "No genome hit"
kkonganti@1:     bcs_sal_yn_prefix = "bettercallsal_salyn"
kkonganti@1:     sal_y = "Detected"
kkonganti@1:     sal_n = "Not detected"
kkonganti@1:     ncbi_pathogens_base_url = "https://www.ncbi.nlm.nih.gov/pathogens/"
kkonganti@1: 
kkonganti@1:     sample2salmon, snp_clusters, multiqc_salmon_counts, seen_sero, sal_yn = (
kkonganti@1:         defaultdict(defaultdict),
kkonganti@1:         defaultdict(defaultdict),
kkonganti@1:         defaultdict(defaultdict),
kkonganti@1:         defaultdict(int),
kkonganti@1:         defaultdict(int),
kkonganti@1:     )
kkonganti@1: 
kkonganti@1:     cell_colors_yml = {
kkonganti@1:         bcs_sal_yn_prefix: {sal_y: "#c8e6c9 !important;", sal_n: "#ffcdd2 !important;"}
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     salmon_comb_res = os.path.join(os.getcwd(), out_prefix + ".txt")
kkonganti@1:     bcs_sal_yn = re.sub(out_prefix, bcs_sal_yn_prefix + ".tblsum", salmon_comb_res)
kkonganti@1:     cell_colors_yml_file = re.sub(
kkonganti@1:         out_prefix + ".txt", bcs_sal_yn_prefix + ".cellcolors.yml", salmon_comb_res
kkonganti@1:     )
kkonganti@1:     salmon_comb_res_mqc = os.path.join(os.getcwd(), str(out_prefix).split(".")[0] + "_mqc.json")
kkonganti@1:     salmon_res_files = glob.glob(os.path.join(salmon_res_dir, "*", "quant.sf"), recursive=True)
kkonganti@1:     salmon_res_file_failed = glob.glob(os.path.join(salmon_res_dir, "BCS_NO_CALLS.txt"))
kkonganti@1: 
kkonganti@1:     if rtc and (not os.path.exists(rtc) or not os.path.getsize(rtc) > 0):
kkonganti@1:         logging.error(
kkonganti@1:             "The reference target cluster metadata file,\n"
kkonganti@1:             + f"{os.path.basename(rtc)} does not exist or is empty!"
kkonganti@1:         )
kkonganti@1:         exit(1)
kkonganti@1: 
kkonganti@1:     if rtc and (not salmon_res_dir or not pickled_sero):
kkonganti@1:         logging.error("When -rtc is on, -sal and -ps are also required.")
kkonganti@1:         exit(1)
kkonganti@1: 
kkonganti@1:     if pickled_sero and (not os.path.exists(pickled_sero) or not os.path.getsize(pickled_sero)):
kkonganti@1:         logging.error(
kkonganti@1:             "The pickle file,\n" + f"{os.path.basename(pickled_sero)} does not exist or is empty!"
kkonganti@1:         )
kkonganti@1:         exit(1)
kkonganti@1: 
kkonganti@1:     if salmon_res_dir:
kkonganti@1:         if not os.path.isdir(salmon_res_dir):
kkonganti@1:             logging.error("UNIX path\n" + f"{salmon_res_dir}\n" + "does not exist!")
kkonganti@1:             exit(1)
kkonganti@1:         if len(salmon_res_files) <= 0:
kkonganti@1:             # logging.error(
kkonganti@1:             #     "Parent directory,\n"
kkonganti@1:             #     + f"{salmon_res_dir}"
kkonganti@1:             #     + "\ndoes not seem to have any directories that contain\n"
kkonganti@1:             #     + "the `quant.sf` file(s)."
kkonganti@1:             # )
kkonganti@1:             # exit(1)
kkonganti@1:             with open(salmon_comb_res, "w") as salmon_comb_res_fh:
kkonganti@1:                 salmon_comb_res_fh.write(f"Sample\n{no_hit}s in any samples\n")
kkonganti@1:             salmon_comb_res_fh.close()
kkonganti@1:             exit(0)
kkonganti@1: 
kkonganti@1:     if rtc and os.path.exists(rtc) and os.path.getsize(rtc) > 0:
kkonganti@1: 
kkonganti@1:         # pdg_release = re.match(r"(^PDG\d+\.\d+)\..+", os.path.basename(rtc))[1] + "/"
kkonganti@1:         acc2sero = pickle.load(file=open(pickled_sero, "rb"))
kkonganti@1: 
kkonganti@1:         with open(rtc, "r") as rtc_fh:
kkonganti@1: 
kkonganti@1:             for line in rtc_fh:
kkonganti@1:                 cols = line.strip().split("\t")
kkonganti@1: 
kkonganti@1:                 if len(cols) < 4:
kkonganti@1:                     logging.error(
kkonganti@1:                         f"The file {os.path.basename(rtc)} seems to\n"
kkonganti@1:                         + "be malformed. It contains less than required 4 columns."
kkonganti@1:                     )
kkonganti@1:                     exit(1)
kkonganti@1:                 elif cols[3] != "NULL":
kkonganti@1:                     snp_clusters[cols[0]].setdefault("assembly_accs", []).append(cols[3])
kkonganti@1:                     snp_clusters[cols[3]].setdefault("snp_clust_id", []).append(cols[0])
kkonganti@1:                     snp_clusters[cols[3]].setdefault("pathdb_acc_id", []).append(cols[1])
kkonganti@1:                     if len(snp_clusters[cols[3]]["snp_clust_id"]) > 1:
kkonganti@1:                         logging.error(
kkonganti@1:                             f"There is a duplicate reference accession [{cols[3]}]"
kkonganti@1:                             + f"in the metadata file{os.path.basename(rtc)}!"
kkonganti@1:                         )
kkonganti@1:                         exit(1)
kkonganti@1: 
kkonganti@1:         rtc_fh.close()
kkonganti@1: 
kkonganti@1:         for salmon_res_file in salmon_res_files:
kkonganti@1:             sample_name = re.match(
kkonganti@1:                 r"(^.+?)((\_salmon\_res)|(\.salmon))$",
kkonganti@1:                 os.path.basename(os.path.dirname(salmon_res_file)),
kkonganti@1:             )[1]
kkonganti@1:             salmon_meta_json = os.path.join(
kkonganti@1:                 os.path.dirname(salmon_res_file), "aux_info", "meta_info.json"
kkonganti@1:             )
kkonganti@1: 
kkonganti@1:             if not os.path.exists(salmon_meta_json) or not os.path.getsize(salmon_meta_json) > 0:
kkonganti@1:                 logging.error(
kkonganti@1:                     "The file\n"
kkonganti@1:                     + f"{salmon_meta_json}\ndoes not exist or is empty!\n"
kkonganti@1:                     + "Did `salmon quant` fail?"
kkonganti@1:                 )
kkonganti@1:                 exit(1)
kkonganti@1: 
kkonganti@1:             if not os.path.exists(salmon_res_file) or not os.path.getsize(salmon_res_file):
kkonganti@1:                 logging.error(
kkonganti@1:                     "The file\n"
kkonganti@1:                     + f"{salmon_res_file}\ndoes not exist or is empty!\n"
kkonganti@1:                     + "Did `salmon quant` fail?"
kkonganti@1:                 )
kkonganti@1:                 exit(1)
kkonganti@1: 
kkonganti@1:             with open(salmon_res_file, "r") as salmon_res_fh:
kkonganti@1:                 for line in salmon_res_fh.readlines():
kkonganti@1:                     if re.match(r"^Name.+", line):
kkonganti@1:                         continue
kkonganti@1:                     cols = line.strip().split("\t")
kkonganti@1:                     ref_acc = "_".join(cols[0].split("_")[:2])
kkonganti@1:                     (
kkonganti@1:                         sample2salmon[sample_name]
kkonganti@1:                         .setdefault(acc2sero[cols[0]], [])
kkonganti@1:                         .append(int(round(float(cols[4]), 2)))
kkonganti@1:                     )
kkonganti@1:                     (
kkonganti@1:                         sample2salmon[sample_name]
kkonganti@1:                         .setdefault("snp_clust_ids", {})
kkonganti@1:                         .setdefault("".join(snp_clusters[ref_acc]["snp_clust_id"]), [])
kkonganti@1:                         .append("".join(snp_clusters[ref_acc]["pathdb_acc_id"]))
kkonganti@1:                     )
kkonganti@1:                     seen_sero[acc2sero[cols[0]]] = 1
kkonganti@1: 
kkonganti@1:             salmon_meta_json_read = json.load(open(salmon_meta_json, "r"))
kkonganti@1:             (
kkonganti@1:                 sample2salmon[sample_name]
kkonganti@1:                 .setdefault("tot_reads", [])
kkonganti@1:                 .append(salmon_meta_json_read["num_processed"])
kkonganti@1:             )
kkonganti@1: 
kkonganti@1:         with open(salmon_comb_res, "w") as salmon_comb_res_fh:
kkonganti@1: 
kkonganti@1:             # snp_clust_col_header = (
kkonganti@1:             #     "\tSNP Cluster(s) by Genome Hit\n" if show_snp_clust_col else "\n"
kkonganti@1:             # )
kkonganti@1:             snp_clust_col_header = (
kkonganti@1:                 "\tNCBI Pathogens Isolate Browser\n" if show_snp_clust_col else "\n"
kkonganti@1:             )
kkonganti@1:             serotypes = sorted(seen_sero.keys())
kkonganti@1:             formatted_serotypes = [
kkonganti@1:                 re.sub(r"\,antigen_formula=", " | ", s)
kkonganti@1:                 for s in [re.sub(r"serotype=", "", s) for s in serotypes]
kkonganti@1:             ]
kkonganti@1:             salmon_comb_res_fh.write(
kkonganti@1:                 "Sample\t" + "\t".join(formatted_serotypes) + snp_clust_col_header
kkonganti@1:             )
kkonganti@1:             # sample_snp_relation = (
kkonganti@1:             #     ncbi_pathogens_base_url
kkonganti@1:             #     + pdg_release
kkonganti@1:             #     + "".join(snp_clusters[ref_acc]["snp_clust_id"])
kkonganti@1:             #     + "?accessions="
kkonganti@1:             # )
kkonganti@1:             sample_snp_relation = ncbi_pathogens_base_url + "isolates/#"
kkonganti@1: 
kkonganti@1:             if len(salmon_res_file_failed) == 1:
kkonganti@1:                 with (open("".join(salmon_res_file_failed), "r")) as no_calls_fh:
kkonganti@1:                     for line in no_calls_fh.readlines():
kkonganti@1:                         if line in ["\n", "\n\r", "\r"]:
kkonganti@1:                             continue
kkonganti@1:                         salmon_comb_res_fh.write(line.strip())
kkonganti@1:                         sal_yn[line.strip()] += 0
kkonganti@1:                         for serotype in serotypes:
kkonganti@1:                             salmon_comb_res_fh.write("\t-")
kkonganti@1:                         salmon_comb_res_fh.write(
kkonganti@1:                             "\t-\n"
kkonganti@1:                         ) if show_snp_clust_col else salmon_comb_res_fh.write("\n")
kkonganti@1:                 no_calls_fh.close()
kkonganti@1: 
kkonganti@1:             for sample, counts in sorted(sample2salmon.items()):
kkonganti@1:                 salmon_comb_res_fh.write(sample)
kkonganti@1:                 snp_cluster_res_col = list()
kkonganti@1: 
kkonganti@1:                 for snp_clust_id in sample2salmon[sample]["snp_clust_ids"].keys():
kkonganti@1:                     # print(snp_clust_id)
kkonganti@1:                     # print(",".join(sample2salmon[sample]["snp_clust_ids"][snp_clust_id]))
kkonganti@1:                     # ppp.pprint(sample2salmon[sample]["snp_clust_ids"])
kkonganti@1:                     # ppp.pprint(sample2salmon[sample]["snp_clust_ids"][snp_clust_id])
kkonganti@1:                     # final_url_text = ",".join(
kkonganti@1:                     #     sample2salmon[sample]["snp_clust_ids"][snp_clust_id]
kkonganti@1:                     # )
kkonganti@1:                     # final_url_text_to_show = snp_clust_id
kkonganti@1:                     # snp_cluster_res_col.append(
kkonganti@1:                     #     "".join(
kkonganti@1:                     #         [
kkonganti@1:                     #             f'<a href="',
kkonganti@1:                     #             sample_snp_relation,
kkonganti@1:                     #             ",".join(sample2salmon[sample]["snp_clust_ids"][snp_clust_id]),
kkonganti@1:                     #             f'" target="_blank">{snp_clust_id}</a>',
kkonganti@1:                     #         ]
kkonganti@1:                     #     )
kkonganti@1:                     # )
kkonganti@1:                     final_url_text_to_show = " ".join(
kkonganti@1:                         sample2salmon[sample]["snp_clust_ids"][snp_clust_id]
kkonganti@1:                     )
kkonganti@1:                     snp_cluster_res_col.append(
kkonganti@1:                         "".join(
kkonganti@1:                             [
kkonganti@1:                                 f'<a href="',
kkonganti@1:                                 sample_snp_relation,
kkonganti@1:                                 final_url_text_to_show,
kkonganti@1:                                 f'" target="_blank">{final_url_text_to_show}</a>',
kkonganti@1:                             ]
kkonganti@1:                         )
kkonganti@1:                     )
kkonganti@1: 
kkonganti@1:                 per_serotype_counts = 0
kkonganti@1:                 for serotype in serotypes:
kkonganti@1: 
kkonganti@1:                     if serotype in sample2salmon[sample].keys():
kkonganti@1:                         # ppp.pprint(counts)
kkonganti@1:                         sample_perc_mapped = round(
kkonganti@1:                             sum(counts[serotype]) / sum(counts["tot_reads"]) * 100, 2
kkonganti@1:                         )
kkonganti@1:                         salmon_comb_res_fh.write(
kkonganti@1:                             f"\t{sum(counts[serotype])} ({sample_perc_mapped}%)"
kkonganti@1:                         )
kkonganti@1:                         multiqc_salmon_counts[sample].setdefault(
kkonganti@1:                             re.match(r"^serotype=(.+?)\,antigen_formula.*", serotype)[1],
kkonganti@1:                             sum(counts[serotype]),
kkonganti@1:                         )
kkonganti@1:                         per_serotype_counts += sum(counts[serotype])
kkonganti@1:                         sal_yn[sample] += 1
kkonganti@1:                     else:
kkonganti@1:                         salmon_comb_res_fh.write(f"\t-")
kkonganti@1:                         sal_yn[sample] += 0
kkonganti@1: 
kkonganti@1:                 multiqc_salmon_counts[sample].setdefault(
kkonganti@1:                     no_hit, sum(counts["tot_reads"]) - per_serotype_counts
kkonganti@1:                 )
kkonganti@1:                 snp_clust_col_val = (
kkonganti@1:                     f'\t{" ".join(snp_cluster_res_col)}\n' if show_snp_clust_col else "\n"
kkonganti@1:                 )
kkonganti@1:                 # ppp.pprint(multiqc_salmon_counts)
kkonganti@1:                 salmon_comb_res_fh.write(snp_clust_col_val)
kkonganti@1: 
kkonganti@1:             with open(bcs_sal_yn, "w") as bcs_sal_yn_fh:
kkonganti@1:                 bcs_sal_yn_fh.write("Sample\tSalmonella Presence\tNo. of Serotypes\n")
kkonganti@1:                 for sample in sal_yn.keys():
kkonganti@1:                     if sal_yn[sample] > 0:
kkonganti@1:                         bcs_sal_yn_fh.write(f"{sample}\tDetected\t{sal_yn[sample]}\n")
kkonganti@1:                     else:
kkonganti@1:                         bcs_sal_yn_fh.write(f"{sample}\tNot detected\t{sal_yn[sample]}\n")
kkonganti@1: 
kkonganti@1:             with open(cell_colors_yml_file, "w") as cell_colors_fh:
kkonganti@1:                 yaml.dump(cell_colors_yml, cell_colors_fh, default_flow_style=False)
kkonganti@1: 
kkonganti@1:             salmon_plot_json(salmon_comb_res_mqc, multiqc_salmon_counts, no_hit)
kkonganti@1: 
kkonganti@1:         salmon_comb_res_fh.close()
kkonganti@1:         bcs_sal_yn_fh.close()
kkonganti@1:         cell_colors_fh.close()
kkonganti@1: 
kkonganti@1: 
kkonganti@1: def salmon_plot_json(file: None, sample_salmon_counts: None, no_hit: None) -> None:
kkonganti@1:     """
kkonganti@1:     This method will take a dictionary of salmon counts per sample
kkonganti@1:     and will dump a JSON that will be used by MultiQC.
kkonganti@1:     """
kkonganti@1: 
kkonganti@1:     if file is None or sample_salmon_counts is None:
kkonganti@1:         logging.error(
kkonganti@1:             "Neither an output file to dump the JSON for MultiQC or the"
kkonganti@1:             + "dictionary holding the salmon counts was not passed."
kkonganti@1:         )
kkonganti@1: 
kkonganti@1:     # Credit: http://phrogz.net/tmp/24colors.html
kkonganti@1:     # Will cycle through 20 distinct colors.
kkonganti@1:     distinct_color_palette = [
kkonganti@1:         "#FF0000",
kkonganti@1:         "#FFFF00",
kkonganti@1:         "#00EAFF",
kkonganti@1:         "#AA00FF",
kkonganti@1:         "#FF7F00",
kkonganti@1:         "#BFFF00",
kkonganti@1:         "#0095FF",
kkonganti@1:         "#FF00AA",
kkonganti@1:         "#FFD400",
kkonganti@1:         "#6AFF00",
kkonganti@1:         "#0040FF",
kkonganti@1:         "#EDB9B9",
kkonganti@1:         "#B9D7ED",
kkonganti@1:         "#E7E9B9",
kkonganti@1:         "#DCB9ED",
kkonganti@1:         "#B9EDE0",
kkonganti@1:         "#8F2323",
kkonganti@1:         "#23628F",
kkonganti@1:         "#8F6A23",
kkonganti@1:         "#6B238F",
kkonganti@1:         "#4F8F23",
kkonganti@1:     ]
kkonganti@1: 
kkonganti@1:     no_hit_color = "#434348"
kkonganti@1:     col_count = 0
kkonganti@1:     serotypes = set()
kkonganti@1:     salmon_counts = defaultdict(defaultdict)
kkonganti@1:     salmon_counts["id"] = "BETTERCALLSAL_SALMON_COUNTS"
kkonganti@1:     salmon_counts["section_name"] = "Salmon read counts"
kkonganti@1:     salmon_counts["description"] = (
kkonganti@1:         "This section shows the read counts from running <code>salmon</code> "
kkonganti@1:         + "in <code>--meta</code> mode using SE, merged PE or concatenated PE reads against "
kkonganti@1:         + "an on-the-fly <code>salmon</code> index generated from the genome hits "
kkonganti@1:         + "of <code>kma</code>."
kkonganti@1:     )
kkonganti@1:     salmon_counts["plot_type"] = "bargraph"
kkonganti@1:     salmon_counts["pconfig"]["id"] = "bettercallsal_salmon_counts_plot"
kkonganti@1:     salmon_counts["pconfig"]["title"] = "Salmon: Read counts"
kkonganti@1:     salmon_counts["pconfig"]["ylab"] = "Number of reads"
kkonganti@1:     salmon_counts["pconfig"]["xDecimals"] = "false"
kkonganti@1:     salmon_counts["pconfig"]["cpswitch_counts_label"] = "Number of reads (Counts)"
kkonganti@1:     salmon_counts["pconfig"]["cpswitch_percent_label"] = "Number of reads (Percentages)"
kkonganti@1: 
kkonganti@1:     for sample in sorted(sample_salmon_counts.keys()):
kkonganti@1:         serotypes.update(list(sample_salmon_counts[sample].keys()))
kkonganti@1:         salmon_counts["data"][sample] = sample_salmon_counts[sample]
kkonganti@1: 
kkonganti@1:     for serotype in sorted(serotypes):
kkonganti@1:         if serotype == no_hit:
kkonganti@1:             continue
kkonganti@1:         if col_count == len(distinct_color_palette) - 1:
kkonganti@1:             col_count = 0
kkonganti@1: 
kkonganti@1:         col_count += 1
kkonganti@1:         salmon_counts["categories"][serotype] = {"color": distinct_color_palette[col_count]}
kkonganti@1: 
kkonganti@1:     salmon_counts["categories"][no_hit] = {"color": no_hit_color}
kkonganti@1:     json.dump(salmon_counts, open(file, "w"))
kkonganti@1: 
kkonganti@1: 
kkonganti@1: if __name__ == "__main__":
kkonganti@1:     main()