def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE TSS enrichment.')
parser.add_argument('--read-len-log',
type=str,
help='Read length log file (from aligner task).')
parser.add_argument('--nodup-bam',
type=str,
help='Raw BAM file (from task filter).')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--tss', type=str, help='TSS definition bed file.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
help='Log level',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
])
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE DCC Count signal track generation')
parser.add_argument('ta', type=str, help='Path for TAGALIGN file.')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file.')
parser.add_argument(
'--mem-gb',
type=float,
default=4.0,
help='Max. memory for this job in GB. '
'This will be used to determine GNU sort -S (defaulting to 0.5 of this value). '
'It should be total memory for this task (not memory per thread).')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE frac mito',
description='Calculates fraction of mito reads')
parser.add_argument('non_mito_samstat',
type=str,
help='Path for SAMstats log file')
parser.add_argument('mito_samstat',
type=str,
help='Path for SAMstats log file (mito only)')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Calling peaks macs2...')
npeak = macs2(
args.ta,
args.chrsz,
args.gensz,
args.pval_thresh,
args.smooth_win,
args.cap_num_peak,
args.mem_gb,
args.out_dir,
)
log.info('Checking if output is empty...')
assert_file_not_empty(npeak)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE compare signal to roadmap')
parser.add_argument('--bigwig',
type=str,
help='BIGWIG file (from task macs2).')
parser.add_argument('--dnase', type=str, help='DNase file.')
parser.add_argument('--reg2map', type=str, help='Reg2map file.')
parser.add_argument('--reg2map-bed', type=str, help='Reg2map bed file.')
parser.add_argument('--roadmap-meta',
type=str,
help='Roadmap metadata file.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
help='Log level',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
])
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE preseq')
parser.add_argument('--paired-end',
action="store_true",
help='Paired-end BAM.')
parser.add_argument('--bam', type=str, help='Raw BAM file.')
parser.add_argument('--picard-java-heap',
help='Picard\'s Java max. heap: java -jar picard.jar '
'-Xmx[MAX_HEAP]')
parser.add_argument('--nth',
type=int,
default=1,
help='Number of threads to parallelize.')
parser.add_argument(
'--mem-gb',
type=float,
help='Max. memory for samtools sort in GB. '
'It should be total memory for this task (not memory per thread).')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
help='Log level',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
])
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE DCC control TAG-ALIGN subsampler.'
'This script does not check if number of reads in TA is higher than '
'subsampling number (--subsample). '
'If number of reads in TA is lower than subsampling number then '
'TA will be just shuffled.')
parser.add_argument('ta', type=str,
help='Path for control TAGALIGN file.')
parser.add_argument('--paired-end', action="store_true",
help='Paired-end TAGALIGN.')
parser.add_argument('--subsample', default=0, type=int,
help='Number of reads to subsample.')
parser.add_argument('--out-dir', default='', type=str,
help='Output directory.')
parser.add_argument('--log-level', default='INFO',
choices=['NOTSET', 'DEBUG', 'INFO',
'WARNING', 'CRITICAL', 'ERROR',
'CRITICAL'],
help='Log level')
args = parser.parse_args()
if not args.subsample:
raise ValueError('--subsample should be a positive integer.')
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC MACS2 signal track',
description='')
parser.add_argument('ta', type=str,
help='Path for TAGALIGN file.')
parser.add_argument('--chrsz', type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--gensz', type=str,
help='Genome size (sum of entries in 2nd column of \
chr. sizes file, or hs for human, ms for mouse).')
parser.add_argument('--pval-thresh', default=0.01, type=float,
help='P-Value threshold.')
parser.add_argument('--smooth-win', default=150, type=int,
help='Smoothing window size.')
parser.add_argument('--mem-gb', type=float, default=4.0,
help='Max. memory for this job in GB. '
'This will be used to determine GNU sort -S (defaulting to 0.5 of this value). '
'It should be total memory for this task (not memory per thread).')
parser.add_argument('--out-dir', default='', type=str,
help='Output directory.')
parser.add_argument('--log-level', default='INFO',
choices=['NOTSET', 'DEBUG', 'INFO',
'WARNING', 'CRITICAL', 'ERROR',
'CRITICAL'],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def main():
# read params
args = parse_arguments()
ALIGNED_BAM = args.bam
OUTPUT_PREFIX = os.path.join(args.out_dir,
os.path.basename(strip_ext_bam(ALIGNED_BAM)))
RG_FREE_ALIGNED_BAM = remove_read_group(ALIGNED_BAM)
JAVA_HEAP = args.picard_java_heap
# Library complexity: Preseq results, NRF, PBC1, PBC2
if args.paired_end:
picard_est_lib_size = get_picard_complexity_metrics(
RG_FREE_ALIGNED_BAM, OUTPUT_PREFIX, JAVA_HEAP)
else:
picard_est_lib_size = None
preseq_data, preseq_log = run_preseq(ALIGNED_BAM,
OUTPUT_PREFIX) # SORTED BAM
get_preseq_plot(preseq_data, OUTPUT_PREFIX)
# write picard_est_lib_size to file
if picard_est_lib_size is not None:
picard_est_lib_size_file = OUTPUT_PREFIX + '.picard_est_lib_size.qc'
with open(picard_est_lib_size_file, 'w') as fp:
fp.write(str(picard_est_lib_size) + '\n')
rm_f(RG_FREE_ALIGNED_BAM)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def main():
# read params
args = parse_arguments()
REF = args.ref_fa
FINAL_BAM = args.nodup_bam
OUTPUT_PREFIX = os.path.join(
args.out_dir,
os.path.basename(strip_ext_bam(FINAL_BAM)))
RG_FREE_FINAL_BAM = remove_read_group(FINAL_BAM)
JAVA_HEAP = args.picard_java_heap
gc_out, gc_plot_pdf, gc_summary = get_gc(RG_FREE_FINAL_BAM,
REF,
OUTPUT_PREFIX,
JAVA_HEAP)
# will generate PNG format from gc_out
plot_gc(gc_out, OUTPUT_PREFIX)
rm_f(RG_FREE_FINAL_BAM)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE DCC Naive overlap.',
description='NarrowPeak or RegionPeak only.')
parser.add_argument('peak1', type=str, help='Peak 1.')
parser.add_argument('peak2', type=str, help='Peak 2.')
parser.add_argument('peak_pooled', type=str, help='Pooled peak.')
parser.add_argument('--prefix',
default='overlap',
type=str,
help='Prefix basename for output overlap peak.')
parser.add_argument(
'--peak-type',
type=str,
required=True,
choices=['narrowPeak', 'regionPeak', 'broadPeak', 'gappedPeak'],
help='Peak file type.')
parser.add_argument('--nonamecheck',
action='store_true',
help='bedtools intersect -nonamecheck. \
use this if you get bedtools intersect \
naming convenction warnings/errors).')
parser.add_argument('--blacklist', type=str, help='Blacklist BED file.')
parser.add_argument('--regex-bfilt-peak-chr-name',
help='Keep chromosomes matching this pattern only '
'in .bfilt. peak files.')
parser.add_argument('--ta', type=str, help='TAGALIGN file for FRiP.')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--fraglen',
type=int,
default=0,
help='Fragment length for TAGALIGN file. \
If given, do shifted FRiP (for ChIP-Seq).')
parser.add_argument(
'--mem-gb',
type=float,
default=4.0,
help='Max. memory for this job in GB. '
'This will be used to determine GNU sort -S (defaulting to 0.5 of this value). '
'It should be total memory for this task (not memory per thread).')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
if args.blacklist is None or args.blacklist.endswith('null'):
args.blacklist = ''
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC MACS2 signal track',
description='')
parser.add_argument('tas', type=str, nargs='+',
help='Path for TAGALIGN file (first) and control TAGALIGN file (second; optional).')
parser.add_argument('--fraglen', type=int, required=True,
help='Fragment length.')
parser.add_argument('--shift', type=int, default=0,
help='macs2 callpeak --shift.')
parser.add_argument('--chrsz', type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--gensz', type=str,
help='Genome size (sum of entries in 2nd column of \
chr. sizes file, or hs for human, ms for mouse).')
parser.add_argument('--pval-thresh', default=0.01, type=float,
help='P-Value threshold.')
parser.add_argument('--out-dir', default='', type=str,
help='Output directory.')
parser.add_argument('--log-level', default='INFO',
choices=['NOTSET', 'DEBUG', 'INFO',
'WARNING', 'CRITICAL', 'ERROR',
'CRITICAL'],
help='Log level')
args = parser.parse_args()
if len(args.tas) == 1:
args.tas.append('')
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC pseudo replicator.')
parser.add_argument('ta', type=str, help='Path for TAGALIGN file.')
parser.add_argument('--paired-end',
action="store_true",
help='Paired-end TAGALIGN.')
parser.add_argument(
'--pseudoreplication-random-seed',
type=int,
default=0,
help='Set it to 0 to use file\'s size (in bytes) as random seed.'
'Otherwise this seed will be used for GNU shuf --random-source=sha256(seed).'
'It is useful when random seed based on input file size does not work.'
)
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC Blacklist filter.')
parser.add_argument('peak', type=str, help='Peak file.')
parser.add_argument('--blacklist',
type=str,
required=True,
help='Blacklist BED file.')
parser.add_argument('--keep-irregular-chr',
action="store_true",
help='Keep reads with non-canonical chromosome names.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
if args.blacklist.endswith('null'):
args.blacklist = ''
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE spp call_peak')
parser.add_argument(
'tas', type=str, nargs=2,
help='Path for TAGALIGN file and control TAGALIGN file.')
parser.add_argument('--chrsz', type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--fraglen', type=int, required=True,
help='Fragment length.')
parser.add_argument('--fdr-thresh', default=0.01, type=float,
help='FDR threshold for run_spp.R -fdr parameter.')
parser.add_argument('--cap-num-peak', default=300000, type=int,
help='Capping number of peaks by taking top N peaks.')
parser.add_argument('--nth', type=int, default=1,
help='Number of threads to parallelize.')
parser.add_argument('--out-dir', default='', type=str,
help='Output directory.')
parser.add_argument('--log-level', default='INFO',
choices=['NOTSET', 'DEBUG', 'INFO',
'WARNING', 'CRITICAL', 'ERROR',
'CRITICAL'],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC MACS2 signal track',
description='')
parser.add_argument('ta', type=str, help='Path for TAGALIGN file.')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--gensz',
type=str,
help='Genome size (sum of entries in 2nd column of \
chr. sizes file, or hs for human, ms for mouse).')
parser.add_argument('--pval-thresh',
default=0.01,
type=float,
help='P-Value threshold.')
parser.add_argument('--smooth-win',
default=73,
type=int,
help='Smoothing window size.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Making self-pseudo replicates...')
if args.paired_end:
ta_pr1, ta_pr2 = spr_pe(
args.ta,
args.pseudoreplication_random_seed,
args.out_dir,
)
else:
ta_pr1, ta_pr2 = spr_se(
args.ta,
args.pseudoreplication_random_seed,
args.out_dir,
)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(ta_pr1)
assert_file_not_empty(ta_pr2)
log.info('All done.')
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC FRiP.', description='')
parser.add_argument('peak', type=str, help='Peak file.')
parser.add_argument('ta', type=str, help='TAGALIGN file.')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file. \
If given, do shifted FRiP (for ChIP-Seq).')
parser.add_argument('--fraglen',
type=int,
default=0,
help='Fragment length for TAGALIGN file. \
If given, do shifted FRiP (for ChIP-Seq).')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC TAGALIGN pooler.',
description='')
parser.add_argument('tas',
nargs='+',
type=str,
help='List of TAGALIGNs to be pooled.')
parser.add_argument('--prefix', type=str, help='Basename prefix.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--col',
help='Number of columns to keep in a pooled TAGALIGN. '
'Keep all columns if not defined.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC Blacklist filter.')
parser.add_argument('peak', type=str, help='Peak file.')
parser.add_argument('--blacklist', type=str, help='Blacklist BED file.')
parser.add_argument('--regex-bfilt-peak-chr-name',
help='Keep chromosomes matching this pattern only '
'in .bfilt. peak files.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
if args.blacklist is None or args.blacklist.endswith('null'):
args.blacklist = ''
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir_R1)
if args.paired_end:
mkdir_p(args.out_dir_R2)
log.info('Cropping fastqs ({} bp) with Trimmomatic...'.format(
args.crop_length))
if args.paired_end:
cropped_R1, cropped_R2 = trimmomatic_pe(args.fastq1, args.fastq2,
args.crop_length,
args.out_dir_R1,
args.out_dir_R2, args.nth,
args.trimmomatic_java_heap)
else:
cropped_R1 = trimmomatic_se(args.fastq1, args.crop_length,
args.out_dir_R1, args.nth,
args.trimmomatic_java_heap)
log.info('List all files in output directory...')
ls_l(args.out_dir_R1)
if args.paired_end:
ls_l(args.out_dir_R2)
log.info('Checking if output is empty...')
assert_file_not_empty(
cropped_R1,
help='No reads in FASTQ after cropping. crop_length might be too high? '
'While cropping, Trimmomatic (with MINLEN) excludes all reads '
'SHORTER than crop_length.')
log.info('All done.')
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE post align', description='')
parser.add_argument('fastq', type=str, help='Path for FASTQ R1')
parser.add_argument('bam', type=str, help='Path for BAM')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file. If not given then '
'SAMstats on mito-free BAM will not be calcaulted.')
parser.add_argument('--mito-chr-name',
default='chrM',
help='Mito chromosome name.')
parser.add_argument('--nth',
type=int,
default=1,
help='Number of threads to parallelize.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='Wrapper for BSUB job submission for ATAC-seq data.',
description='')
parser.add_argument('--path-to-fastqs',
default='',
type=str,
help='Path to FASTQ files.')
parser.add_argument('--memory',
default='10GB',
type=str,
help='Memory requested to run the analysis.')
parser.add_argument(
'--queue',
default='standard',
type=str,
help='Queue to submit the job in HPCF (use bqueues to choose).')
parser.add_argument('--out-dir', type=str, help='Output Directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC filter.')
parser.add_argument('bam', type=str, help='Path for raw BAM file.')
parser.add_argument('--dup-marker',
type=str,
choices=['picard', 'sambamba'],
default='picard',
help='Dupe marker for filtering mapped reads in BAM.')
parser.add_argument('--mapq-thresh',
default=30,
type=int,
help='Threshold for low MAPQ reads removal.')
parser.add_argument('--no-dup-removal',
action="store_true",
help='No dupe reads removal when filtering BAM.')
parser.add_argument('--paired-end',
action="store_true",
help='Paired-end BAM.')
parser.add_argument('--multimapping',
default=0,
type=int,
help='Multimapping reads.')
parser.add_argument(
'--filter-chrs',
nargs='*',
help='Chromosomes to be filtered for final (nodup/filt) BAM.')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--mito-chr-name',
default='chrM',
help='Mito chromosome name.')
parser.add_argument('--nth',
type=int,
default=1,
help='Number of threads to parallelize.')
parser.add_argument(
'--mem-gb',
type=float,
help='Max. memory for samtools sort in GB. '
'It should be total memory for this task (not memory per thread).')
parser.add_argument('--picard-java-heap',
help='Picard\'s Java max. heap: java -jar picard.jar '
'-Xmx[MAX_HEAP]')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE annot_enrich (fraction of reads in annotated regions)')
parser.add_argument('--ta',
type=str,
help='TAG-ALIGN file (from task bam2ta).')
parser.add_argument('--dnase', type=str, help='DNase definition bed file.')
parser.add_argument('--blacklist', type=str, help='Blacklist bed file.')
parser.add_argument('--prom',
type=str,
help='Promoter definition bed file.')
parser.add_argument('--enh',
type=str,
help='Enhancer definition bed file.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
help='Log level',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
])
args = parser.parse_args()
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE post_call_peak (chip)',
description='')
parser.add_argument('peak', type=str,
help='Path for PEAK file. Peak filename should be "*.*Peak.gz". '
'e.g. rep1.narrowPeak.gz')
parser.add_argument('--ta', type=str,
help='TAG-ALIGN file.')
parser.add_argument('--peak-type', type=str, required=True,
choices=['narrowPeak', 'regionPeak',
'broadPeak', 'gappedPeak'],
help='Peak file type.')
parser.add_argument('--fraglen', type=int, required=True,
help='Fragment length.')
parser.add_argument('--chrsz', type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--blacklist', type=str, required=True,
help='Blacklist BED file.')
parser.add_argument('--keep-irregular-chr', action="store_true",
help='Keep reads with non-canonical chromosome names.')
parser.add_argument('--out-dir', default='', type=str,
help='Output directory.')
parser.add_argument('--log-level', default='INFO',
choices=['NOTSET', 'DEBUG', 'INFO',
'WARNING', 'CRITICAL', 'ERROR',
'CRITICAL'],
help='Log level')
args = parser.parse_args()
if args.blacklist.endswith('/dev/null'):
args.blacklist = ''
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Calling peaks with macs2...')
npeak = macs2(
args.tas[0],
args.tas[1],
args.chrsz,
args.gensz,
args.pval_thresh,
args.shift,
args.fraglen,
args.cap_num_peak,
args.ctl_subsample,
args.ctl_paired_end,
args.mem_gb,
args.out_dir,
)
log.info('Checking if output is empty...')
assert_file_not_empty(npeak)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC bwa aligner.',
description='')
parser.add_argument('bwa_index_prefix_or_tar', type=str,
help='Path for prefix (or a tarball .tar) \
for reference bwa index. \
Prefix must be like [PREFIX].sa. \
TAR ball can have any [PREFIX] but it should not \
have a directory structure in it.')
parser.add_argument('fastqs', nargs='+', type=str,
help='List of FASTQs (R1 and R2). \
FASTQs must be compressed with gzip (with .gz).')
parser.add_argument(
'--use-bwa-mem-for-pe', action="store_true",
help='Use "bwa mem" for PAIRED-ENDED dataset with R1 FASTQ\'s read length >= --bwa-mem-read-len-limit. '
'For shorter reads, bwa aln will be used. ')
parser.add_argument(
'--rescue-reads-for-bwa-mem', action="store_true",
help='Use -P for "bwa mem" to rescue missing hits only (by using SW algorithm) '
'but do not try to find hits that fit a proper pair.'
)
parser.add_argument('--bwa-mem-read-len-limit', type=int, default=70,
help='Read length limit for bwa mem (for paired-ended FASTQs only). '
'bwa aln will be used instead of bwa mem if R1 reads are shorter than this.')
parser.add_argument('--paired-end', action="store_true",
help='Paired-end FASTQs.')
parser.add_argument('--nth', type=int, default=1,
help='Number of threads to parallelize.')
parser.add_argument('--mem-gb', type=float,
help='Max. memory for samtools sort and GNU sort -S '
'(half of this value will be used for GNU sort) in GB. '
'It should be total memory for this task (not memory per thread).')
parser.add_argument('--out-dir', default='', type=str,
help='Output directory.')
parser.add_argument('--log-level', default='INFO',
choices=['NOTSET', 'DEBUG', 'INFO',
'WARNING', 'CRITICAL', 'ERROR',
'CRITICAL'],
help='Log level')
args = parser.parse_args()
# check if fastqs have correct dimension
if args.paired_end and len(args.fastqs) != 2:
raise argparse.ArgumentTypeError('Need 2 fastqs for paired end.')
if not args.paired_end and len(args.fastqs) != 1:
raise argparse.ArgumentTypeError('Need 1 fastq for single end.')
if args.use_bwa_mem_for_pe and not args.paired_end:
raise ValueError(
'--use-bwa-mem-for-pe is for paired ended FASTQs only.'
)
if not args.use_bwa_mem_for_pe and args.rescue_reads_for_bwa_mem:
raise ValueError(
'--rescue-reads-for-bwa-mem is available only when --use-bwa-mem-for-pe is activated.'
)
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE DCC Naive overlap.',
description='NarrowPeak or RegionPeak only.')
parser.add_argument('peak1', type=str, help='Peak 1.')
parser.add_argument('peak2', type=str, help='Peak 2.')
parser.add_argument('peak_pooled', type=str, help='Pooled peak.')
parser.add_argument('--prefix',
default='overlap',
type=str,
help='Prefix basename for output overlap peak.')
parser.add_argument(
'--peak-type',
type=str,
required=True,
choices=['narrowPeak', 'regionPeak', 'broadPeak', 'gappedPeak'],
help='Peak file type.')
parser.add_argument('--nonamecheck',
action='store_true',
help='bedtools intersect -nonamecheck. \
use this if you get bedtools intersect \
naming convenction warnings/errors).')
parser.add_argument('--blacklist',
type=str,
required=True,
help='Blacklist BED file.')
parser.add_argument('--keep-irregular-chr',
action="store_true",
help='Keep reads with non-canonical chromosome names.')
parser.add_argument('--ta', type=str, help='TAGALIGN file for FRiP.')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--fraglen',
type=int,
default=0,
help='Fragment length for TAGALIGN file. \
If given, do shifted FRiP (for ChIP-Seq).')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
if args.blacklist.endswith('/dev/null'):
args.blacklist = ''
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE DCC IDR.', description='NarrowPeak or RegionPeak only.')
parser.add_argument('peak1', type=str, help='Peak file 1.')
parser.add_argument('peak2', type=str, help='Peak file 2.')
parser.add_argument('peak_pooled', type=str, help='Pooled peak file.')
parser.add_argument('--prefix',
default='idr',
type=str,
help='Prefix basename for output IDR peak.')
parser.add_argument(
'--peak-type',
type=str,
required=True,
choices=['narrowPeak', 'regionPeak', 'broadPeak', 'gappedPeak'],
help='Peak file type.')
parser.add_argument('--idr-thresh',
default=0.1,
type=float,
help='IDR threshold.')
parser.add_argument('--idr-rank',
default='p.value',
type=str,
choices=['p.value', 'q.value', 'signal.value'],
help='IDR ranking method.')
parser.add_argument('--blacklist', type=str, help='Blacklist BED file.')
parser.add_argument('--regex-bfilt-peak-chr-name',
help='Keep chromosomes matching this pattern only '
'in .bfilt. peak files.')
parser.add_argument('--ta', type=str, help='TAGALIGN file for FRiP.')
parser.add_argument('--chrsz',
type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--fraglen',
type=int,
default=0,
help='Fragment length for TAGALIGN file. \
If given, do shifted FRiP (for ChIP-Seq).')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
if args.blacklist is None or args.blacklist.endswith('null'):
args.blacklist = ''
log.setLevel(args.log_level)
log.info(sys.argv)
return args
