Mercurial > repos > estrain > data_manager_mlst

annotate data_manager/data_manager_mlst.py @ 0:a9ff6184213f draft default tip

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planemo upload commit bdb45cf3a98e21f5002866b6789a1457f521bf5d
author estrain
date Thu, 12 Mar 2026 20:06:31 +0000
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1 #!/usr/bin/env python3
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2 """
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3 Galaxy Data Manager for PubMLST.
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4 Downloads all PubMLST databases, creates a combined BLAST database,
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5 and writes a Galaxy-compatible data table JSON.
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6 """
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7
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8 import argparse
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9 import json
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10 import os
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11 import shutil
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12 import subprocess
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13 import sys
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14 import datetime
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15 from urllib.request import urlopen
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16
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17
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18 class MLSTDataManager:
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19 def __init__(self, json_path: str):
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20 self.json_path = json_path
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21 self.extra_files_path = None
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22 self.output_dir = None
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23 self.timestamp = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
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24 self.db_name = f"mlst_database_{self.timestamp}"
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25
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26 # ----------------------------------------------------------------------
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27 # Galaxy JSON I/O
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28 # ----------------------------------------------------------------------
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29
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30 def read_input_json(self):
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31 """Read Galaxy input JSON and create the output directory."""
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32 with open(self.json_path) as fh:
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33 params = json.load(fh)
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34 self.extra_files_path = params["output_data"][0]["extra_files_path"]
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35 os.makedirs(self.extra_files_path, exist_ok=True)
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36 self.output_dir = os.path.abspath(self.extra_files_path)
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37
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38 def write_output_json(self):
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39 """Write the final Galaxy data manager JSON."""
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40 entry = {
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41 "data_tables": {
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42 "mlst": [
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43 {
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44 "value": self.db_name,
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45 "name": self.db_name,
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46 "path": "mlst-db"
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47 }
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48 ]
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49 }
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50 }
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51
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52 with open(self.json_path, "w") as fh:
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53 json.dump(entry, fh, indent=2, sort_keys=True)
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54 fh.flush()
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55 os.fsync(fh.fileno())
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56
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57 # ----------------------------------------------------------------------
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58 # Database steps
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59 # ----------------------------------------------------------------------
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60
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61 def download_pubmlst_databases(self):
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62 """Download all PubMLST databases."""
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63 print("Downloading PubMLST databases...")
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64 try:
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65 subprocess.run(["mlst-download_pub_mlst", "-d", "pubmlst"], check=True)
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66 except subprocess.CalledProcessError as e:
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67 print(f"Error downloading databases: {e}")
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68 sys.exit(1)
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69
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70 def make_blast_database(self):
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71 """Build a BLAST database from the downloaded data."""
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72 cwd = os.getcwd()
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73 src_dir = os.path.join(cwd, "pubmlst")
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74 dst_dir = os.path.join(self.output_dir, "pubmlst")
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75
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76 if os.path.exists(dst_dir):
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77 shutil.rmtree(dst_dir)
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78 shutil.move(src_dir, dst_dir)
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79
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80 blast_dir = os.path.join(self.output_dir, "blast")
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81 os.makedirs(blast_dir, exist_ok=True)
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82 blast_file = os.path.join(blast_dir, "mlst.fa")
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83
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84 print("Building combined FASTA for BLAST database...")
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85 with open(blast_file, "a") as outfile:
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86 for scheme in os.listdir(dst_dir):
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87 scheme_path = os.path.join(dst_dir, scheme)
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88 if os.path.isdir(scheme_path):
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89 for f in os.listdir(scheme_path):
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90 if f.endswith(".tfa"):
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91 with open(os.path.join(scheme_path, f)) as infile:
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92 for line in infile:
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93 if "not a locus" not in line:
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94 if line.startswith(">"):
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95 outfile.write(f">{scheme}.{line[1:]}")
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96 else:
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97 outfile.write(line)
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98
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99 print("Running makeblastdb...")
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100 subprocess.run([
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101 "makeblastdb", "-hash_index",
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102 "-in", blast_file, "-dbtype", "nucl",
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103 "-title", "PubMLST", "-parse_seqids"
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104 ], check=True)
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105
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106 def download_scheme_species_map(self):
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107 """Fetch the scheme_species_map.tab file from GitHub."""
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108 url = "https://raw.githubusercontent.com/tseemann/mlst/master/db/scheme_species_map.tab"
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109 dst_file = os.path.join(self.output_dir, "scheme_species_map.tab")
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110 print("Downloading scheme_species_map.tab...")
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111 try:
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112 with urlopen(url) as response, open(dst_file, "w") as out:
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113 out.write(response.read().decode("utf-8"))
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114 print("scheme_species_map.tab downloaded successfully")
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115 except Exception as e:
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116 print(f"Failed to retrieve scheme_species_map.tab: {e}")
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117
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118 # ----------------------------------------------------------------------
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119 # Run
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120 # ----------------------------------------------------------------------
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121
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122 def run(self):
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123 try:
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124 self.read_input_json()
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125 self.download_pubmlst_databases()
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126 self.make_blast_database()
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127 self.download_scheme_species_map()
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128 except Exception as e:
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129 print(f"MLST Data Manager failed: {e}")
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130 finally:
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131 self.write_output_json()
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132
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133
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134 # ----------------------------------------------------------------------
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135 # CLI
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136 # ----------------------------------------------------------------------
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137
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138 def parse_args():
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139 parser = argparse.ArgumentParser(description="Galaxy Data Manager for PubMLST")
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140 parser.add_argument("data_manager_json", help="Galaxy data manager JSON file")
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141 return parser.parse_args()
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142
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143
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144 def main():
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145 args = parse_args()
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146 mgr = MLSTDataManager(args.data_manager_json)
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147 mgr.run()
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148
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149
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150 if __name__ == "__main__":
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151 main()
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152