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86 lines
4.0 KiB
Python
86 lines
4.0 KiB
Python
'''
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Author & Date: Adri K. Grow + ChatGPT, Nov 11th 2024
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- Updated 02/13/25 to accept either transcriptome and genome assembled data in command line
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Motivation: assess and rename assembled transcript or genome files for use in EukPhylo Part 1
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Intention: warn if any 'transcripts.fasta' or 'contigs.fasta' files are missing or empty for an LKH, otherwise rename and copy them with their assigned 10-digit code by LKH
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Input:
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- a base directory containing subdirectories for each LKH assembled file, named 'WTA_LKH<xxxx>' or 'WGA_LKH<xxxx>', each containing a 'transcripts.fasta' or 'contigs.fasta' file
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- a mapping .txt file with LKH#s tab-separated with corresponding 10-digit codes
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Output:
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- a folder named 'renamed_transcripts|contigs' with assembled files now named by 10-digit codes; e.g. "Sr_rh_Ro04_assembledTranscripts.fasta"
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Dependencies: python3
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Usage:
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- for transcriptomes: python3 ProcessAndRenameAssembledData.py <assembled transcriptomes directory> <mapping_file.txt> transcriptomes
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- for genomes: python3 ProcessAndRenameAssembledData.py <assembled genomes directory> <mapping_file.txt> genomes
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'''
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import os
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import shutil
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import sys
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def read_lkh_mapping(mapping_file):
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"""Reads the LKH number to 10-digit code mapping from a file."""
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mapping = {}
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with open(mapping_file, 'r') as file:
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for line in file:
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lkh_number, code = line.strip().split('\t')
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mapping[lkh_number] = code
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return mapping
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def process_directory(base_dir, mapping, output_dir, data_type):
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"""Iterates over all subdirectories in base_dir, processes relevant fasta files."""
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if not os.path.exists(output_dir):
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os.makedirs(output_dir) # Create output directory if it doesn't exist
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# Set file naming patterns based on data type
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folder_prefix = "WTA_LKH" if data_type == "transcriptomes" else "WGA_LKH"
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fasta_filename = "transcripts.fasta" if data_type == "transcriptomes" else "contigs.fasta"
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output_suffix = "_assembledTranscripts.fasta" if data_type == "transcriptomes" else "_assembledContigs.fasta"
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for folder_name in os.listdir(base_dir):
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folder_path = os.path.join(base_dir, folder_name)
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if os.path.isdir(folder_path) and folder_name.startswith(folder_prefix):
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lkh_number = folder_name.split('_')[1] # Extract LKH number from folder name
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fasta_file = os.path.join(folder_path, fasta_filename)
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if not os.path.isfile(fasta_file):
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print(f" WARNING: file '{fasta_filename}' is missing in folder {folder_name}.")
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continue
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if os.path.getsize(fasta_file) == 0:
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print(f" WARNING: file '{fasta_filename}' is empty in folder {folder_name}.")
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continue
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if lkh_number in mapping:
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new_name = f"{mapping[lkh_number]}{output_suffix}"
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output_path = os.path.join(output_dir, new_name)
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shutil.copy(fasta_file, output_path)
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else:
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print(f"Notification: No 10-digit code found for LKH number {lkh_number} in folder {folder_name}.")
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def main():
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if len(sys.argv) != 4 or sys.argv[3] not in ["transcriptomes", "genomes"]:
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print("Usage: python script.py <base_dir> <mapping_file> <transcriptomes|genomes>")
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sys.exit(1)
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base_dir = sys.argv[1]
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mapping_file = sys.argv[2]
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data_type = sys.argv[3]
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if not os.path.isdir(base_dir):
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print(f"Error: The directory '{base_dir}' does not exist.")
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sys.exit(1)
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if not os.path.isfile(mapping_file):
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print(f"Error: The file '{mapping_file}' does not exist.")
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sys.exit(1)
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output_dir = os.path.join(os.getcwd(), "renamed_transcripts" if data_type == "transcriptomes" else "renamed_contigs")
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mapping = read_lkh_mapping(mapping_file)
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process_directory(base_dir, mapping, output_dir, data_type)
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if __name__ == "__main__":
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main()
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