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comparison microrunqc/mlstAddFields.py @ 25:4f457838f4c9 draft default tip

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Fixed missing tab in MLST report
author estrain
date Wed, 28 Feb 2024 01:16:18 +0000
parents dc12d6ac296d
children
comparison
equal deleted inserted replaced
24:dc12d6ac296d 25:4f457838f4c9
19 19
20 # Return the output without appending if schema equals "-" 20 # Return the output without appending if schema equals "-"
21 if schema == "-": 21 if schema == "-":
22 print("\t".join(mlstout)) 22 print("\t".join(mlstout))
23 return 23 return
24 24
25 if db_path is None: 25 if db_path is None:
26 # If no database path is provided, find it using an external command 26 # If no database path is provided, find it using an external command
27 # This requires the 'mlst' command to be installed and available in the path 27 # This requires the 'mlst' command to be installed and available in the path
28 import subprocess 28 import subprocess
29 mlstdesc = subprocess.check_output(['mlst', '-h']).decode() 29 mlstdesc = subprocess.check_output(['mlst', '-h']).decode()
60 schema_dict[line[0]] = ','.join(desc) 60 schema_dict[line[0]] = ','.join(desc)
61 61
62 output = mlstout[:3] 62 output = mlstout[:3]
63 if mlstST in schema_dict: 63 if mlstST in schema_dict:
64 output.append(schema_dict[mlstST]) 64 output.append(schema_dict[mlstST])
65 else:
66 output.append("-")
65 output.extend(mlstout[3:]) 67 output.extend(mlstout[3:])
66 68
67 print("\t".join(output)) 69 print("\t".join(output))
68 70
69 if __name__ == "__main__": 71 if __name__ == "__main__":