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1 #!/usr/bin/env python3
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2
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3 # Kranti Konganti
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4
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5 import argparse
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6 import inspect
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7 import logging
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8 import os
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9 import re
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10 import shutil
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11 import ssl
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12 import tempfile
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13 from html.parser import HTMLParser
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14 from urllib.request import urlopen
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15
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16 # Set logging.f
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17 logging.basicConfig(
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18 format="\n" + "=" * 55 + "\n%(asctime)s - %(levelname)s\n" + "=" * 55 + "\n%(message)s\n",
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19 level=logging.DEBUG,
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20 )
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21
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22 # Multiple inheritence for pretty printing of help text.
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23 class MultiArgFormatClasses(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
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24 pass
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25
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26
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27 # HTMLParser override class to get PDG release and latest Cluster .tsv file
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28 class NCBIPathogensHTMLParser(HTMLParser):
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29 def __init__(self, *, convert_charrefs: bool = ...) -> None:
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30 super().__init__(convert_charrefs=convert_charrefs)
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31 self.reset()
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32 self.href_data = list()
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33
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34 def handle_data(self, data):
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35 self.href_data.append(data)
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36
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37
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38 def dl_pdg(**kwargs) -> None:
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39 """
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40 Method to save the PDG metadata file and
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41 return the latest PDG release.
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42 """
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43 db_path, url, regex, suffix, overwrite, release = [kwargs[k] for k in kwargs.keys()]
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44
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45 contxt = ssl.create_default_context()
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46 contxt.check_hostname = False
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47 contxt.verify_mode = ssl.CERT_NONE
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48
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49 if (db_path or url) == None:
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50 logging.error("Please provide absolute UNIX path\n" + "to store the result DB flat files.")
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51 exit(1)
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52
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53 if re.match(r"^PDG\d+\.\d+$", release):
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54 url = re.sub("latest_snps", release.strip(), url)
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55
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56 html_parser = NCBIPathogensHTMLParser()
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57 logging.info(f"Finding latest NCBI PDG release at:\n{url}")
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58
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59 with urlopen(url, context=contxt) as response:
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60 with tempfile.NamedTemporaryFile(delete=False) as tmp_html_file:
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61 shutil.copyfileobj(response, tmp_html_file)
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62
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63 with open(tmp_html_file.name, "r") as html:
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64 html_parser.feed("".join(html.readlines()))
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65
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66 pdg_filename = re.search(regex, "".join(html_parser.href_data)).group(0)
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67 pdg_release = pdg_filename.rstrip(suffix)
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68 pdg_metadata_url = "/".join([url, pdg_filename])
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69 pdg_release = pdg_filename.rstrip(suffix)
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70 dest_dir = os.path.join(db_path, pdg_release)
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71
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72 logging.info(f"Found NCBI PDG file:\n{pdg_metadata_url}")
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73
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74 if (
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75 not overwrite
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76 and re.match(r".+?\.metadata\.tsv$", pdg_filename)
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77 and os.path.exists(dest_dir)
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78 ):
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79 logging.error(f"DB path\n{dest_dir}\nalready exists. Please use -f to overwrite.")
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80 exit(1)
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81 elif overwrite and not re.match(r".+?\.reference_target\.cluster_list\.tsv$", pdg_filename):
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82 shutil.rmtree(dest_dir, ignore_errors=True) if os.path.exists(dest_dir) else None
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83 os.makedirs(dest_dir)
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84 elif (
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85 not overwrite
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86 and re.match(r".+?\.metadata\.tsv$", pdg_filename)
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87 and not os.path.exists(dest_dir)
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88 ):
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89 os.makedirs(dest_dir)
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90
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91 tsv_at = os.path.join(dest_dir, pdg_filename)
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92 logging.info(f"Saving to:\n{tsv_at}")
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93
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94 with urlopen(pdg_metadata_url, context=contxt) as response:
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95 with open(tsv_at, "w") as tsv:
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96 tsv.writelines(response.read().decode("utf-8"))
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97
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98 html.close()
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99 tmp_html_file.close()
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100 os.unlink(tmp_html_file.name)
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101 tsv.close()
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102 response.close()
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103
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104 return tsv_at, dest_dir
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105
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106
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107 def main() -> None:
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108 """
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109 This script is part of the `bettercallsal_db` Nextflow workflow and is only
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110 tested on POSIX sytems.
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111 It:
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112 1. Downloads the latest NCBI Pathogens Release metadata file, which
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113 looks like PDGXXXXXXXXXX.2504.metadata.csv and also the SNP cluster
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114 information file which looks like PDGXXXXXXXXXX.2504.reference_target.cluster_list.tsv
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115 2. Generates a new metadata file with only required information such as
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116 computed_serotype, isolates GenBank or RefSeq downloadable genome FASTA
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117 URL.
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118 """
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119
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120 prog_name = os.path.basename(inspect.stack()[0].filename)
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121
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122 parser = argparse.ArgumentParser(
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123 prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
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124 )
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125
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126 # required = parser.add_argument_group("required arguments")
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127
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128 parser.add_argument(
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129 "-db",
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130 dest="db_path",
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131 default=os.getcwd(),
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132 required=False,
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133 help="Absolute UNIX path to a path where all results files are\nstored.",
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134 )
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135 parser.add_argument(
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136 "-f",
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137 dest="overwrite_db",
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138 default=False,
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139 required=False,
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140 action="store_true",
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141 help="Force overwrite a PDG release directory at DB path\nmentioned with -db.",
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142 )
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143 parser.add_argument(
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144 "-org",
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145 dest="organism",
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146 default="Salmonella",
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147 required=False,
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148 help="The organism to create the DB flat files\nfor.",
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149 )
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150 parser.add_argument(
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151 "-rel",
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152 dest="release",
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153 default=False,
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154 required=False,
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155 help="If you get a 404 error, try mentioning the actual release identifier.\n"
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156 + "Ex: For Salmonella, you can get the release identifier by going to:\n"
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157 + " https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella\n"
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158 + "Ex: If you want metadata beloginging to release PDG000000002.2507, then you\n"
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159 + " would use this command-line option as:\n -rel PDG000000002.2507",
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160 )
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161
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162 args = parser.parse_args()
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163 db_path = args.db_path
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164 org = args.organism
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165 overwrite = args.overwrite_db
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166 release = args.release
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167 ncbi_pathogens_loc = "/".join(
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168 ["https://ftp.ncbi.nlm.nih.gov/pathogen/Results", org, "latest_snps"]
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169 )
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170
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171 if not db_path:
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172 db_path = os.getcwd()
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173
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174 # Save metadata
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175 file, dest_dir = dl_pdg(
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176 db_path=db_path,
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177 url="/".join([ncbi_pathogens_loc, "Metadata"]),
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178 regex=re.compile(r"PDG\d+\.\d+\.metadata\.tsv"),
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179 suffix=".metadata.tsv",
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180 overwrite=overwrite,
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181 release=release,
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182 )
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183
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184 # Save cluster to target mapping
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185 dl_pdg(
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186 db_path=db_path,
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187 url="/".join([ncbi_pathogens_loc, "Clusters"]),
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188 regex=re.compile(r"PDG\d+\.\d+\.reference_target\.cluster_list\.tsv"),
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189 suffix="reference_target\.cluster_list\.tsv",
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190 overwrite=overwrite,
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191 release=release,
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192 )
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193
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194 # Create accs.txt for dataformat to fetch required ACC fields
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195 accs_file = os.path.join(dest_dir, "accs_all.txt")
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196 with open(file, "r") as pdg_metadata_fh:
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197 with open(accs_file, "w") as accs_fh:
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198 for line in pdg_metadata_fh.readlines():
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199 if re.match(r"^#", line) or line in ["\n", "\n\r", "\r"]:
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200 continue
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201 cols = line.strip().split("\t")
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202 asm_acc = cols[9]
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203 accs_fh.write(f"{asm_acc}\n") if (asm_acc != "NULL") else None
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204 accs_fh.close()
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205 pdg_metadata_fh.close()
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206
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207 logging.info("Finished writing accessions for dataformat tool.")
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208
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209
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210 if __name__ == "__main__":
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211 main()
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