Mercurial > repos > tduigou > seq_from_db

annotate get_db_info.py @ 0:934050a8037e draft

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
author tduigou
date Thu, 17 Jul 2025 09:34:14 +0000
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children 54e716c11b71
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934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
tduigou
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1 import subprocess
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
tduigou
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2 import argparse
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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3 import time
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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4 import json
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5 import os
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6 import socket
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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7 import re
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8 from Bio.Seq import Seq
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9 import pandas as pd
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10 from Bio.SeqRecord import SeqRecord
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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11 from sqlalchemy import create_engine, inspect
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12 from sqlalchemy.engine.url import make_url
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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13 from sqlalchemy.sql import text
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14 from sqlalchemy.exc import OperationalError
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17 def fix_db_uri(uri):
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18 """Replace __at__ with @ in the URI if needed."""
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19 return uri.replace("__at__", "@")
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22 def is_port_in_use(uri):
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23 """Check if a TCP port is already in use on host."""
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24 url = make_url(uri)
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25 host = url.host
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26 port = url.port
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27 with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
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28 s.settimeout(2)
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29 return s.connect_ex((host, port)) == 0
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32 def extract_db_name(uri):
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33 """Extract the database name from the SQLAlchemy URI."""
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34 url = make_url(uri)
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35 return url.database
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37
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38 # this fuction is to activate the Docker id the DB is in container. BUT IT IS NOT USED IN MAIN()
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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39 def start_postgres_container(db_name):
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40 """Start a PostgreSQL container with the given database name as the container name."""
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41 container_name = db_name
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42
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43 # Check if container is already running
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44 container_running = subprocess.run(
934050a8037e planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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45 f"docker ps -q -f name={container_name}", shell=True, capture_output=True, text=True
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46 )
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47
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48 if container_running.stdout.strip():
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49 print(f"Container '{container_name}' is already running.")
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50 return
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51
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52 # Check if container exists (stopped)
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53 container_exists = subprocess.run(
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54 f"docker ps -a -q -f name={container_name}", shell=True, capture_output=True, text=True
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55 )
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56
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57 if container_exists.stdout.strip():
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58 print(f"Starting existing container '{container_name}'...")
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59 subprocess.run(f"docker start {container_name}", shell=True)
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60 print(f"PostgreSQL Docker container '{container_name}' activated.")
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61 return
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62
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63 # If container does not exist, create and start a new one
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64 port = 5432 if not is_port_in_use(5432) else 5433
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65 postgres_password = os.getenv("POSTGRES_PASSWORD", "RK17")
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66
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67 start_command = [
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68 "docker", "run", "--name", container_name,
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69 "-e", f"POSTGRES_PASSWORD={postgres_password}",
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70 "-p", f"{port}:5432",
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71 "-d", "postgres"
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72 ]
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73
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74 try:
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75 subprocess.run(start_command, check=True)
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76 print(f"PostgreSQL Docker container '{container_name}' started on port {port}.")
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77 except subprocess.CalledProcessError as e:
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78 print(f"Failed to start Docker container: {e}")
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79
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80
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81 def wait_for_db(uri, timeout=60):
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82 """Try connecting to the DB until it works or timeout."""
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83 engine = create_engine(uri)
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84 start_time = time.time()
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85 while time.time() - start_time < timeout:
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86 try:
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87 with engine.connect():
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88 print("Connected to database.")
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89 return
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90 except OperationalError:
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91 print("Database not ready, retrying...")
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92 time.sleep(2)
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93 raise Exception("Database connection failed after timeout.")
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94
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95
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96 def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, table_name, fragment_column_name, output):
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97 """Fetch annotations from the database and save the result as GenBank files."""
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98 db_uri = fix_db_uri(db_uri)
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99 df = pd.read_csv(csv_file, sep=',', header=None)
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100
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101 engine = create_engine(db_uri)
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102 connection = engine.connect()
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103
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104 annotated_data = []
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105
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106 try:
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107 with connection:
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108 inspector = inspect(engine)
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109 columns = [column['name'] for column in inspector.get_columns(table_name)]
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110
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111 # Fetch all fragments from the table once
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112 if fragment_column_name not in columns:
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113 raise ValueError(f"Fragment column '{fragment_column_name}' not found in table '{table_name}'.")
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114
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115 fragment_column_index = columns.index(fragment_column_name)
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116 all_rows = connection.execute(text(f"SELECT * FROM {table_name}")).fetchall()
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117 fragment_map = {row[fragment_column_index]: row for row in all_rows}
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118
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119 # Compare fragments between CSV and DB
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120 csv_fragments = set()
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121 all_ids = set(df[0].dropna().astype(str))
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122 for _, row in df.iterrows():
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123 for col in df.columns:
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124 if col != 0:
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125 fragment = row[col]
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126 if pd.notna(fragment):
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127 fragment_str = str(fragment)
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128 if fragment_str not in all_ids:
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129 csv_fragments.add(fragment_str)
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130
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131 db_fragments = set(fragment_map.keys())
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132 missing_fragments = sorted(list(csv_fragments - db_fragments))
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133 if missing_fragments:
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134 raise ValueError(
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135 f" Missing fragments in DB: {', '.join(missing_fragments)}"
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136 )
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137
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138 # === CONTINUE WITH GB FILE CREATION ===
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139 for _, row in df.iterrows():
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140 annotated_row = {"Backbone": row[0], "Fragments": []}
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141 for col in df.columns:
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142 if col != 0:
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143 fragment = row[col]
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144 if fragment not in csv_fragments:
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145 continue
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146 db_row = fragment_map.get(fragment)
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147
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148 if db_row:
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149 fragment_data = {"id": fragment}
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150 for i, column_name in enumerate(columns[1:]): # skip ID column
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151 fragment_data[column_name] = db_row[i + 1]
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152 else:
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153 fragment_data = {"id": fragment, "metadata": "No data found"}
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154
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155 annotated_row["Fragments"].append(fragment_data)
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156
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157 annotated_data.append(annotated_row)
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158
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159 except Exception as e:
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160 print(f"Error occurred during annotation: {e}")
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161 raise # Ensures the error exits the script
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162
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163 # GenBank file generation per fragment
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164 try:
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165 for annotated_row in annotated_data:
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166 backbone_id = annotated_row["Backbone"]
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167 for fragment in annotated_row["Fragments"]:
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168 fragment_id = fragment["id"]
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169 sequence = fragment.get(sequence_column, "")
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170 annotation = fragment.get(annotation_columns, "")
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171
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172 # Create the SeqRecord
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173 record = SeqRecord(
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174 Seq(sequence),
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175 id=fragment_id,
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176 name=fragment_id,
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177 description=f"Fragment {fragment_id} from Backbone {backbone_id}"
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178 )
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179
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180 # Add annotations to GenBank header
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181 record.annotations = {
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182 k: str(fragment[k]) for k in annotation_columns if k in fragment
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183 }
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184
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185 # LOCUS line extraction from annotation (copy-paste the LOCUS from annotation)
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186 locus_line_match = re.search(r"LOCUS\s+.+", annotation)
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187 if locus_line_match:
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188 locus_line = locus_line_match.group()
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189 else:
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190 print(f"LOCUS info missing for fragment {fragment_id}")
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191 locus_line = f"LOCUS {fragment_id: <20} {len(sequence)} bp DNA linear UNK 01-JAN-2025"
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192
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193 # Format sequence as per GenBank standards (with ORIGIN and line breaks)
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194 if "ORIGIN" in sequence:
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195 origin_block = sequence.strip()
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196 else:
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197 # Format sequence as per GenBank standards (with ORIGIN and line breaks)
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198 formatted_sequence = "ORIGIN\n"
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199 seq_str = str(record.seq)
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200 for i in range(0, len(seq_str), 60): # 60 bases per line
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201 line_seq = seq_str[i:i + 60]
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202 formatted_sequence += f"{str(i + 1).rjust(9)} { ' '.join([line_seq[j:j+10] for j in range(0, len(line_seq), 10)]) }\n"
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203 origin_block = formatted_sequence.strip()
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204
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205 # Find and copy the FEATURES section directly from annotation
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206 features_section = ""
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207 features_start = annotation.find("FEATURES")
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208 if features_start != -1:
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209 features_section = annotation[features_start:]
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210
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211 # Writing the GenBank file
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212 if not os.path.exists(output):
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213 os.makedirs(output)
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214
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215 gb_filename = os.path.join(output, f"{fragment_id}.gb")
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216 with open(gb_filename, "w") as f:
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217 # Write the LOCUS line
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218 f.write(locus_line + "\n")
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219 # Write DEFINITION, ACCESSION, and other annotations
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220 f.write(f"DEFINITION {record.description}\n")
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221 f.write(f"ACCESSION {record.id}\n")
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222 f.write(f"VERSION DB\n")
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223 f.write(f"KEYWORDS .\n")
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224 f.write(f"SOURCE .\n")
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225 # Write the FEATURES section directly from annotation
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226 f.write(features_section)
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227 # Write the ORIGIN section
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228 f.write(origin_block + "\n")
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229 f.write("//\n")
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230
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231 except Exception as e:
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232 print(f"Error saving GenBank files: {e}")
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233 return
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234
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235
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236 def main():
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237 parser = argparse.ArgumentParser(description="Fetch annotations from PostgreSQL database and save as JSON.")
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238 parser.add_argument("--input", required=True, help="Input CSV file")
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239 parser.add_argument("--use_json_paramers", required=True, help="Use parameters from JSON: true/false")
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240 parser.add_argument("--sequence_column", required=False, help="DB column contains sequence for ganbank file")
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241 parser.add_argument("--annotation_columns", required=False, help="DB column contains head for ganbank file")
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242 parser.add_argument("--db_uri", required=False, help="Database URI connection string")
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243 parser.add_argument("--table", required=False, help="Table name in the database")
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244 parser.add_argument("--fragment_column", required=False, help="Fragment column name in the database")
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245 parser.add_argument("--output", required=True, help="Output dir for gb files")
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246 parser.add_argument("--json_conf", required=False, help="JSON config file with DB parameters")
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247 args = parser.parse_args()
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248
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249 # get param and chek for json
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250 config_params = {}
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251 use_json = args.use_json_paramers == 'true'
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252 if use_json:
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253 if not args.json_conf:
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254 raise ValueError("You must provide --json_conf when --use_json_paramers is 'true'")
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255 with open(args.json_conf, "r") as f:
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256 config_params = json.load(f)
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257 else:
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258 config_params = {
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259 "table": args.table,
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260 "sequence_column": args.sequence_column,
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261 "annotation_column": args.annotation_columns,
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262 "fragment_column": args.fragment_column,
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263 "db_uri": args.db_uri,
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264 }
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265
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266 # Extract final resolved parameters
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267 table = config_params["table"]
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268 sequence_column = config_params["sequence_column"]
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269 annotation_column = config_params["annotation_column"]
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270 fragment_column = config_params["fragment_column"]
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271 db_uri = fix_db_uri(config_params["db_uri"])
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272
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273 # Wait until the database is ready
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274 db_uri = fix_db_uri(db_uri)
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275 # db_name = extract_db_name(db_uri)
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276 # start_postgres_container(db_name)
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277 MAX_RETRIES = 3
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278 for attempt in range(1, MAX_RETRIES + 1):
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279 try:
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280 wait_for_db(db_uri)
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281 break # Success
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282 except Exception as e:
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283 if attempt == MAX_RETRIES:
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284 print(f"Attempt {attempt} failed: Could not connect to database at {db_uri}.")
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285 raise e
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286 else:
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287 time.sleep(2)
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288
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289 # Fetch annotations from the database and save as gb
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290 fetch_annotations(args.input, sequence_column, annotation_column, db_uri, table, fragment_column, args.output)
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291
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292 if __name__ == "__main__":
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293 main()