- The input and output default is rawReads/samplesubfolder/
- It also returns a table and a plot with the number of reads for each sample, the output by default is Report/figure/data """
# Parser
parser = argparse.ArgumentParser(prog='qcReads.py', description = 'Quality control of data using FastQC')
parser.add_argument('-v', '--version', action='version', version='%(prog)s-'+__version__)
parser.add_argument('--analysis_info_file', help='Text file with details of the analysis. Default=analysis_info.txt', default='analysis_info.txt')
parser.add_argument('--in_dir', help='Path to folder containing fastq files. Default=rawReads/', default='rawReads/')
parser.add_argument('--out_dir', help='Path to out put folder. Default=rawReads/', default='rawReads/')
parser.add_argument('--out_dir_report', help='Path to out put folder. Default=Report/figure/data/', default='Report/figure/data/')
parser.add_argument('--sample_names_file', help='Text file with sample names. Default=sample_names.txt', default='sample_names.txt')
parser.add_argument('--ncores', help='Number of cores to use. Default=8', default='8')
args=parser.parse_args()
# Set path of working directory
ai=functions.read_analysis_info_file(args.analysis_info_file)
path=os.getcwd()
#Ncores
ncores=int(args.ncores)
# Read sample names text file
sample_names_file=args.sample_names_file
sampleNames = functions.read_sample_names(sample_names_file)
# Set input and output directories if not 'rawReads/'
in_dir=path + '/' + args.in_dir
out_dir=path + '/' +args.out_dir
out_dir_report=path + '/' + args.out_dir_report
# Create out_dir_report
__version__='v01'
# created 17/08/2016
if __name__ == '__main__':
# Parser
parser = argparse.ArgumentParser(prog='organizeWorkingDirectory.py',description = 'Organize working directory of the analysis')
parser.add_argument('-v','--version', action='version',version='%(prog)s-'+__version__)
parser.add_argument('--analysis_info_file', help='Text file with details of the analysis. Default=analysis_info.txt', default='analysis_info.txt')
parser.add_argument('--sample_names_file', help='Text file with sample names. Default=sample_names_info.txt', default='sample_names.txt')
parser.add_argument('--in_dir', help='directory with fastq files. Default= corresponding to bcl2fastq_output', default='bcl2fastq_output')
args=parser.parse_args()
# Read analysis info file
ai=functions.read_analysis_info_file(args.analysis_info_file)
# Change dir
os.chdir(ai['project_location'])
# Read sample names
sample_names_file = args.sample_names_file
sampleNames = functions.read_sample_names(sample_names_file)
# Create rawReads folder
# Check if rawReads exists
project_location=ai['project_location']
folders = os.listdir(project_location)
readsFiles = [folders[i] for i, x in enumerate(folders) if re.findall('rawReads',x)]
# print readsFiles