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
functions.make_sure_path_exists(out_dir_report)
# Detect if files are gz
gz = functions.check_gz(in_dir)
# Run fastqc
Parallel(n_jobs=ncores)(delayed(qc_check)(i) for i in sampleNames)
parser.add_argument('--out_dir', help='Path to output folder. Default=countedReads/', default='countedReads/')
parser.add_argument('--mapping_summary_file', help='Mapping summary file. Default=mapping_summary.csv', default='mapping_summary.csv')
args=parser.parse_args()
params_file=args.analysis_info_file
path=functions.read_parameters_file(params_file)['Working directory']
refGenome=functions.read_parameters_file(params_file)['Reference Genome']
strand=functions.read_parameters_file(params_file)['strand']
strand_piccard, strand_htseq = functions.get_strand(strand)
gtfFile=functions.read_parameters_file(params_file)['GTF File']
os.chdir(path)
# Read sample names text file
sampleNames = functions.read_sample_names()
# Set input and output directories if not '/'
in_dir=args.in_dir
out_dir=args.out_dir
functions.make_sure_path_exists(out_dir)
mapping_summary_file=args.mapping_summary_file
# Detect if files are gz
gz = functions.check_gz(in_dir)
# Count command
Parallel(n_jobs=7)(delayed(counting)(i) for i in sampleNames)
# QC
help='Mapping summary file. Default=mapping_summary.csv',
default='mapping_summary.csv')
args = parser.parse_args()
params_file = args.analysis_info_file
path = functions.read_parameters_file(params_file)['Working directory']
refGenome = functions.read_parameters_file(params_file)['Reference Genome']
strand = functions.read_parameters_file(params_file)['strand']
strand_piccard, strand_htseq = functions.get_strand(strand)
gtfFile = functions.read_parameters_file(params_file)['GTF File']
os.chdir(path)
# Read sample names text file
sampleNames = functions.read_sample_names()
# Set input and output directories if not '/'
in_dir = args.in_dir
out_dir = args.out_dir
functions.make_sure_path_exists(out_dir)
mapping_summary_file = args.mapping_summary_file
# Detect if files are gz
gz = functions.check_gz(in_dir)
# Count command
Parallel(n_jobs=7)(delayed(counting)(i) for i in sampleNames)
# QC
os.system("Rscript /usr/local/bin/countsLog_rnaseq.R " + out_dir + ' ' +
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
# Collect fastq files analysis_info_file
if args.in_dir == 'bcl2fastq_output':
allFiles=functions.get_filepaths(ai['project_location'] + '/' + ai[args.in_dir])
fastq=[allFiles[y] for y, x in enumerate(allFiles) if re.findall("fastq.gz", x)]
fastq=[fastq[y] for y,x in enumerate(fastq) if not re.findall('Undetermined', x)]
elif args.in_dir != 'bcl2fastq_output':
allFiles=os.listdir(args.in_dir)
