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Merge pull request #62 from friendsofstrandseq/weber8thomas/fix-slurm…
…-time-issue weber8thomas/fix slurm time issue
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| import os | ||
| import shutil | ||
| import sys | ||
| import pandas as pd | ||
| import logging | ||
|
|
||
| # Set up logging | ||
| logging.basicConfig( | ||
| level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s" | ||
| ) | ||
|
|
||
|
|
||
| def rename_and_copy_fastq_files( | ||
| source_directory, target_directory, sample_name, cell_name | ||
| ): | ||
| if not os.path.exists(target_directory): | ||
| os.makedirs(target_directory, exist_ok=True) | ||
| logging.info(f"Created directory: {target_directory}") | ||
|
|
||
| for filename in os.listdir(source_directory): | ||
| if filename.endswith(".fastq.gz"): | ||
| new_filename = f"{cell_name}-{sample_name}-{filename}" | ||
| if ".1." or ".2." not in new_filename: | ||
| new_filename = new_filename.replace( | ||
| ".fastq.gz", ".1.fastq.gz" | ||
| ) # Format with cell_name and sample_name | ||
|
|
||
| logging.info(f"Target directory: {target_directory}") | ||
| logging.info(f"New filename: {new_filename}") | ||
|
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| source_path = os.path.join(source_directory, filename) | ||
| target_path = os.path.join(target_directory, new_filename) | ||
| shutil.copy2(source_path, target_path) | ||
| logging.info(f"Copied and renamed from {source_path} to {target_path}") | ||
| # exit() | ||
|
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||
|
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| def process_samples(excel_path, source_base_directory, target_base_directory): | ||
| sample_data = pd.read_csv(excel_path, sep="\t") | ||
| # sample_data = sample_data.loc[sample_data["LIBRARY_LAYOUT"] == "SINGLE"] | ||
| sample_data["Sample_Name"] = sample_data["Source Name"].apply( | ||
| lambda x: x.split("_")[0] | ||
| ) | ||
| sample_data = sample_data[ | ||
| ["Sample_Name", "Characteristics[cell line]"] | ||
| ].drop_duplicates() | ||
| print(sample_data) | ||
| exit() | ||
| for index, row in sample_data.iterrows(): | ||
| source_name = row["Sample_Name"] | ||
| cell_line = row["Characteristics[cell line]"] | ||
|
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| source_directory = os.path.join(source_base_directory, source_name, "fastq") | ||
| logging.info(f"Source directory: {source_directory}") | ||
| logging.info(f"Source name: {source_name}") | ||
| logging.info(f"Cell line: {cell_line}") | ||
| logging.info(f"Target base directory: {target_base_directory}") | ||
| target_directory = os.path.join(target_base_directory, cell_line, "fastq") | ||
|
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||
| if os.path.exists(source_directory): | ||
| rename_and_copy_fastq_files( | ||
| source_directory, target_directory, source_name, cell_line | ||
| ) | ||
| else: | ||
| logging.warning(f"Source directory not found: {source_directory}") | ||
|
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|
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| if __name__ == "__main__": | ||
| if len(sys.argv) != 4: | ||
| logging.error( | ||
| "Usage: python script.py <path_to_excel> <source_base_directory> <target_base_directory>" | ||
| ) | ||
| sys.exit(1) | ||
|
|
||
| _, excel_path, source_base_directory, target_base_directory = sys.argv | ||
| process_samples(excel_path, source_base_directory, target_base_directory) |
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