run_parser.py 文件源码

def find_analysis_barcode_file(parent_dir):
    '''
    Find the barcodes file for the analysis
    # analysis_barcode_file="$(find "$analysis_outdir"  -path "*variantCaller_out*" -name "sample_barcode_IDs.tsv" | head -1)"
    '''
    import os
    import fnmatch
    analysis_barcode_file = None
    for root, dirs, files in os.walk(parent_dir):
        if fnmatch.fnmatch(root, "*variantCaller_out*"):
            for file in files:
                if fnmatch.fnmatch(file, "sample_barcode_IDs.tsv"):
                    analysis_barcode_file = os.path.join(root, file)
                    break
    # make sure file exists
    if analysis_barcode_file == None:
        print("ERROR: Analysis barcode file not found")
    pl.file_exists(analysis_barcode_file, kill = True)
    return(analysis_barcode_file)