#########################
if __name__ == '__main__':
parser = argparse.ArgumentParser(description = 'Counting Reads')
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=alignedReads/', default='alignedReads/')
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
parser.add_argument(
'--in_dir',
help='Path to folder containing fastq files. Default=alignedReads/',
default='alignedReads/')
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
os.system("java -jar -Xmx2g ~/picard-tools-1.127/picard.jar CollectAlignmentSummaryMetrics R="+refGenome+" I="+outdir+"/"+i+"Aligned.sortedByCoord.out.bam O="+outdir+"/stat_align"+i+".txt")
#########################
if __name__ == '__main__':
parser = argparse.ArgumentParser(description = 'Mapping reads with BWA')
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=trimmedReads/', default='trimmedReads/')
parser.add_argument('--out_dir', help='Path to out put folder. Default=alignedReads/', default='alignedReads/')
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']
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)
# Detect if files are gz
gz = functions.check_gz(in_dir)
Parallel(n_jobs=8)(delayed(sam2bam)(i) for i in sampleNames)
default='rawReads')
parser.add_argument(
'--readType',
help='Read Type: pairedEnd or singleEnd. Default=pairedEnd',
default='pairedEnd')
parser.add_argument('--out_dir_plots',
help='Path to out put folder. Default=Report/figure',
default='Report/figure')
parser.add_argument(
'--suffix_name',
help='Suffix to optionally put to the output name. Default=',
default='')
args = parser.parse_args()
params_file = args.analysis_info_file
path = functions.read_parameters_file(params_file)['Working directory']
os.chdir(path)
# Read sample names text file
sampleNames = functions.read_sample_names()
# Set input and output directories if not 'rawReads/'
in_dir = args.in_dir
out_dir = args.out_dir
out_dir_plots = args.out_dir_plots
readType = args.readType
suffix_name = args.suffix_name
files = functions.get_filepaths(in_dir)
files = [
files[y] for y, x in enumerate(files)
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=trimmedReads/',
default='trimmedReads/')
parser.add_argument('--out_dir',
help='Path to out put folder. Default=alignedReads/',
default='alignedReads/')
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']
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)
# Detect if files are gz
gz = functions.check_gz(in_dir)
Parallel(n_jobs=8)(delayed(sam2bam)(i) for i in sampleNames)
os.system('macs2 callpeak --broad -s='+fragSize+' -broadCutOff '+broadCutOff+' -q' + qCutOff + ' --bw '+fragSize+' -f '+readFormat+' -c '+indir+'/'+controlSample+'Aligned.sortedByCoord.bam -t '+in_dir+'/'+treatedSample+"Aligned.sortedByCoord.dedup.removed.out.bam -g "+genomeSize+" -n "+treatedSample+"_"+controlSample+"_bampe_q_value_filtered_dedup_00001_pval -outdir "+out_dir)
else:
os.system('macs2 callpeak -s='+fragSize+' -q' + qCutOff + ' --bw '+fragSize+' -f '+readFormat+' -c '+indir+'/'+controlSample+'Aligned.sortedByCoord.bam -t '+in_dir+'/'+treatedSample+"Aligned.sortedByCoord.dedup.removed.out.bam -g "+genomeSize+" -n "+treatedSample+"_"+controlSample+"_bampe_q_value_filtered_dedup_00001_pval -outdir "+out_dir)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description = 'Peaking calling with MACS2')
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=trimmedReads/', default='trimmedReads/')
parser.add_argument('--out_dir', help='Path to out put folder. Default=alignedReads/', default='alignedReads/')
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']
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
readLength=args.read_length
fragSize = args.fragSize
readFormat = args.readFormat
qCutOff = args.qCutoff
broad = args.broad
broadCutOff = args.broadCutOff
parser.add_argument(
'--in_dir',
help='Path to folder containing fastq files. Default=alignedReads/',
default='alignedReads/')
parser.add_argument(
'--out_dir',
help='Path to out put folder. Default=alignedReads/QC/',
default='alignedReads/QC/')
parser.add_argument(
'--out_dir_plots',
help='Path to out put folder to copy plots. Default=Report/figure/',
default='Report/figure/')
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']
bedFile_10k = functions.read_parameters_file(params_file)['BedFile10K']
bedFile = functions.read_parameters_file(params_file)['BedFile']
refFlat = functions.read_parameters_file(params_file)['refFlat']
rRNA_interval_list = functions.read_parameters_file(
params_file)['rRNA_interval_list']
strand = functions.read_parameters_file(params_file)['strand']
strand_piccard, strand_htseq = functions.get_strand(strand)
#if strand == 'reverse':
# strand = 'SECOND_READ_TRANSCRIPTION_STRAND'
#os.chdir(path)
# Read sample names text file
sampleNames = functions.read_sample_names()
