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