def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('unq_paths', nargs='+')
parser.add_argument('-v',
'--verbose',
action='store_true',
help='print the histogram values to stdout')
parser.add_argument(
'-m',
'--max_frag_size',
type=int,
default=500,
help='Maximum fragment size. Longer fragments will be trimmed. [500]')
parser.add_argument(
'--outdir',
'-o',
help='output directory for the histogram figure(s) [None]')
parser.add_argument('--display',
action='store_true',
help='Display histogram plot(s) (plt.show)')
parser.add_argument(
'-L',
'--bed_file',
help='pat: Only output reads overlapping the input BED FILE')
add_GR_args(parser)
return parser.parse_args()
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('input_files', nargs='+')
parser.add_argument('-p',
'--prefix',
help='Prefix of output file',
required=True)
parser.add_argument('-f',
'--force',
action='store_true',
help='Overwrite existing file if existed')
parser.add_argument(
'-T',
'--temp_dir',
help='passed to "sort -m". Useful for merging very large pat files')
parser.add_argument('-v', '--verbose', action='store_true')
parser.add_argument('--labels',
nargs='+',
help='labels for the mixed reads. '
'Default is None')
add_GR_args(parser, bed_file=True)
parser.add_argument(
'--min_len',
type=int,
default=None,
help='consider only reads covering at least MIN_LEN CpG sites [1]')
parser.add_argument(
'--strict',
action='store_true',
help='Truncate reads that start/end outside the given region. '
'Only relevant if "region", "sites" '
'or "bed_file" flags are given.')
args = parser.parse_args()
return args
def add_view_flags(parser, sub_sample=True, out_path=True):
add_GR_args(parser, bed_file=True)
parser.add_argument(
'--strict',
action='store_true',
help='pat: Truncate reads that start/end outside the given region. '
'Only relevant if "region", "sites" '
'or "bed_file" flags are given.')
parser.add_argument(
'--strip',
action='store_true',
help='pat: Remove trailing dots (from beginning/end of reads).')
parser.add_argument(
'--min_len',
type=int,
default=1,
help='pat: Display only reads covering at least MIN_LEN CpG sites [1]')
if sub_sample:
parser.add_argument(
'--sub_sample',
type=float,
metavar='[0.0, 1.0]',
help='pat: subsample from reads. Only supported for pat')
if out_path:
parser.add_argument('-o', '--out_path', help='Output path. [stdout]')
return parser
def add_args(parser):
parser.add_argument('bam', nargs='+')
add_GR_args(parser)
parser.add_argument('--out_dir', '-o', default='.')
parser.add_argument(
'--min_cpg',
type=int,
default=1,
help='Reads covering less than MIN_CPG sites are removed [1]')
parser.add_argument('--debug', '-d', action='store_true')
parser.add_argument('--force',
'-f',
action='store_true',
help='overwrite existing files if exists')
parser.add_argument('--verbose', '-v', action='store_true')
parser.add_argument('-F', '--exclude_flags', type=int,
help='flags to exclude from bam file (samtools view parameter) ' \
f'[{FLAGS_FILTER}]', default=FLAGS_FILTER)
parser.add_argument(
'-q',
'--mapq',
type=int,
help=f'Minimal mapping quality (samtools view parameter) [{MAPQ}]',
default=MAPQ)
parser.add_argument(
'--clip',
type=int,
default=0,
help='Clip for each read the first and last CLIP characters [0]')
add_multi_thread_args(parser)
return parser
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('beta_paths', nargs='+')
parser.add_argument('-f',
'--force',
action='store_true',
help='Overwrite existing files if existed')
parser.add_argument(
'--keep_na',
action='store_true',
help='If set, missing CpG sites are not removed from the output'
' They are assigned with a "-1" value.')
parser.add_argument('-b',
'--bedGraph',
action='store_true',
help='Keep (gzipped) bedGraphs as well as bigwigs')
parser.add_argument(
'--dump_cov',
action='store_true',
help='Generate coverage bigiwig in addition to beta values bigwig')
parser.add_argument(
'-c',
'--min_cov',
type=int,
default=1,
help='Minimal coverage to consider when computing beta values.'
' Default is 1 (include all observations). '
' Sites with less than MIN_COV coverage are considered as missing.')
parser.add_argument('--outdir',
'-o',
default='.',
help='Output directory. [.]')
add_GR_args(parser, bed_file=True)
args = parser.parse_args()
return args
def parse_args(): # todo: seperate args parsing for beta and pat
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('input_files',
nargs='+',
help='A pat.gz file or one or more beta files')
parser.add_argument(
'-d',
'--dists',
action='store_true',
help='print results with distances (kind of log scale)')
parser.add_argument('-t',
'--title',
help='A text to be printed before the results.')
parser.add_argument('-o', '--output', help='beta vis: save plot to file')
parser.add_argument(
'-b',
'--blocks_path',
help='Display blocks borders. If [-b] is specified with no '
'blocks path, default blocks are used.',
nargs='?',
const=default_blocks_path,
default=False)
parser.add_argument("--no_color",
action='store_true',
help='Print without colors.')
parser.add_argument(
'--strict',
action='store_true',
help='Truncate reads that start/end outside the given region. '
'Only relevant for pat files.')
parser.add_argument(
'--max_reps',
'-m',
type=int,
default=10,
help='Pat vis: Display a read at most "max_reps" times, '
'if it is repeating itself. [10]')
parser.add_argument(
'--min_len',
type=int,
default=1,
help=
'Pat vis: Display only reads covering at least MIN_LEN CpG sites [1]')
parser.add_argument(
'--color_scheme',
'-cs',
type=int,
default=256,
help='beta vis: Color scheme. Possible values: 16 or 256 [256]')
parser.add_argument('--plot',
action='store_true',
help='beta vis: plot results in a heatmap.')
parser.add_argument(
'--no_dense',
action='store_true',
help='pat: Do not squeeze multiple reads to every line.\n'
'Each read appears in a different line.')
add_GR_args(parser, required=True)
return parser.parse_args()
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('betas', nargs='+', help='one or more beta files')
parser.add_argument('--plot',
action='store_true',
help='Plot histogram of coverages')
add_GR_args(parser, bed_file=True)
add_multi_thread_args(parser)
args = parser.parse_args()
return args
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('betas', nargs='+')
parser.add_argument(
'--min_cov',
'-c',
type=int,
default=10,
help='Minimal coverage to consider. '
'Sites with coverage lower than this value are ignored')
add_GR_args(parser)
args = parser.parse_args()
return args
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('betas', nargs='+', help='one or more beta files')
parser.add_argument('--plot',
action='store_true',
help='Plot histogram of coverages')
add_GR_args(parser)
parser.add_argument(
'-L',
'--bed_file',
help='Only output coverage overlapping the input BED FILE. ')
args = parser.parse_args()
return args
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
region_or_sites = add_GR_args(parser, bed_file=True, no_anno=True)
region_or_sites.add_argument('--site_file',
help='text file with a single CpG indexes column,' \
' or <startCpG, endCpG> columns.\n' \
'if "-" is passed, the file is read from stdin.')
parser.add_argument('--out_path',
'-o',
help='Output path for bed file [stdout]')
parser.add_argument('-d', '--debug', action='store_true')
# parser.add_argument('--bedtools', action='store_true')
parser.add_argument(
'-p',
'--parsable',
action='store_true',
help='Output a parsing friendly format (only work with -r/-s flags)')
parser.add_argument('--drop_empty',
action='store_true',
help='Drop empty regions (without CpGs)')
parser.add_argument('-f',
'--force',
action='store_true',
help='Overwrite existing files if existed')
add_multi_thread_args(parser)
args = parser.parse_args()
return args
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('beta_paths', nargs='+')
parser.add_argument('-f',
'--force',
action='store_true',
help='Overwrite existing files if existed')
parser.add_argument('-d', '--debug', action='store_true')
parser.add_argument(
'--outdir',
'-o',
default='.',
help='Output directory. Default is current directory [.]')
add_GR_args(parser)
args = parser.parse_args()
return args
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('input_file')
add_GR_args(parser)
parser.add_argument('-o',
'--out_path',
type=argparse.FileType('w'),
default=sys.stdout,
help='Output path. [stdout]')
parser.add_argument(
'--sub_sample',
type=float,
metavar='(0.0, 1.0)',
help='pat: subsample from reads. Only supported for pat'
) # todo: support unq too
parser.add_argument(
'-L',
'--bed_file',
help='pat: Only output reads overlapping the input BED FILE')
parser.add_argument(
'--strict',
action=
'store_true', # todo: add fractions to trimmed reads (optional flag)
help='pat: Truncate reads that start/end outside the given region. '
'Only relevant if "region", "sites" '
'or "bed_file" flags are given.')
parser.add_argument('--inflate',
action='store_true',
help='unq: add CpG-Index column to the output')
parser.add_argument('--awk_engine',
action='store_true',
help='pat: use awk engine instead of python.\n'
'Its saves RAM when dealing with large regions.')
parser.add_argument(
'--multiprocess',
type=int,
default=16,
help=
'pat: If bed file is specified, use multiple processors to read multiple.\n'
'regions in parallel. Default number of processors: 16.')
parser.add_argument(
'--min_len',
type=int,
default=1,
help='Pat: Display only reads covering at least MIN_LEN CpG sites [1]')
args = parser.parse_args()
return args
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('beta_path')
parser.add_argument('-f', '--force', action='store_true',
help='Overwrite existing files if existed')
parser.add_argument('--keep_na', action='store_true',
help='If set, missing CpG sites are not removed from the output')
parser.add_argument('--mean', action='store_true',
help='Output a mean methylation value column instead of <meth,cov> columns')
parser.add_argument('-c', '--min_cov', type=int, default=1,
help='Minimal coverage to consider when computing beta values.'
' Default is 1 (include all observations). '
' Sites with less than MIN_COV coverage are considered as missing.'
' Only relevant if --mean is specified.')
parser.add_argument('--outpath', '-o', default='/dev/stdout', help='Output path. [stdout]')
add_GR_args(parser, bed_file=True)
args = parser.parse_args()
return args
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('bam_path')
add_GR_args(parser)
parser.add_argument('--out_dir', '-o', default='.')
parser.add_argument('--debug', '-d', action='store_true')
parser.add_argument(
'-@',
'--threads',
type=int,
default=multiprocessing.cpu_count(),
help='Number of threads to use (default: multiprocessing.cpu_count)')
parser.add_argument(
'--test',
action='store_true',
help='Perform a test for the pipeline. Ignore other parameters.')
args = parser.parse_args()
return args
def add_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('pat', help="The input pat file")
add_GR_args(parser, bed_file=True, required=True)
add_multi_thread_args(parser)
parser.add_argument(
'--strict',
action='store_true',
help='Truncate reads that start/end outside the given region.')
parser.add_argument(
'--min_len',
type=int,
default=1,
help='Only use reads covering at least MIN_LEN CpG sites [1]')
parser.add_argument('--out_file',
'-o',
default="-",
help="Output file name in which to write results")
parser.add_argument('--verbose', '-v', action='store_true')
return parser
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('betas', nargs='+')
parser.add_argument(
'--outpath',
'-o',
help=
'Dump figure to this path (e.g., pdf/png). If not specified, --show flag is set'
)
parser.add_argument(
'--show',
action='store_true',
help='Display the figures using matplotlib.pyplot.show.')
parser.add_argument(
'--min_cov',
'-c',
type=int,
default=10,
help='Minimal coverage to consider. '
'Sites with coverage lower than this value are ignored')
add_GR_args(parser)
args = parser.parse_args()
return args
def parse_args(): # todo: seperate args parsing for beta and pat
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('input_files',
nargs='+',
help='A pat.gz file or one or more beta files')
parser.add_argument('-t',
'--title',
help='A text to be printed before the results.')
parser.add_argument(
'-b',
'--blocks_path',
help='Display blocks borders. If [-b] is specified with no '
'blocks path, default blocks are used.',
nargs='?',
const=True,
default=False)
parser.add_argument("--no_color",
action='store_true',
help='Print without colors.')
add_GR_args(parser, required=True, no_anno=True)
pat_args(parser)
beta_args(parser)
return parser
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
add_GR_args(parser, bed_file=True)
betas_or_file = parser.add_mutually_exclusive_group(required=True)
betas_or_file.add_argument('--betas', nargs='+')
betas_or_file.add_argument('--beta_file', '-F')
parser.add_argument('-c',
'--chunk_size',
type=int,
default=DEF_CHUNK,
help=f'Chunk size. Default {DEF_CHUNK} sites')
parser.add_argument(
'-p',
'--pcount',
type=float,
default=15,
help='Pseudo counts of C\'s and T\'s in each block. Default 15')
parser.add_argument('--min_cpg', type=int, default=1,
help='Minimal block size (in #sites) to output. Shorter blocks will simply be ' \
'ommited from output (equivalent to set min_cpg to 1 and then filter output by ' \
'length). Default is 1')
parser.add_argument(
'--max_cpg',
type=int,
default=1000,
help='Maximal allowed block size (in #sites). Default is 1000')
parser.add_argument(
'--max_bp',
type=int,
default=2000,
help='Maximal allowed block size (in bp). Default is 2000')
parser.add_argument('-o',
'--out_path',
default=sys.stdout,
help='output path [stdout]')
add_multi_thread_args(parser)
return parser.parse_args()
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
add_GR_args(parser)
# todo: allow bed file input
parser.add_argument('-L',
'--bed_path',
help='convert all regions in a bed file')
parser.add_argument('--out_path',
'-o',
help='Output path for bed file [stdout]')
parser.add_argument('-d', '--debug', action='store_true')
parser.add_argument('-f',
'--force',
action='store_true',
help='Overwrite existing files if existed')
parser.add_argument(
'-@',
'--threads',
type=int,
default=multiprocessing.cpu_count(),
help='Number of threads to use (default: multiprocessing.cpu_count)')
args = parser.parse_args()
return args
def add_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('bam', help="The full path of the bam file to process")
parser.add_argument('homog_prop', help="A fraction with which to determine homogenous reads. All reads with "
"methylation proportion >= [homog_prop] will be classified as highly "
"methylated reads while all reads with methylation proportion <= 1 - [homog_prop] "
"will be classified as mostly un-methylated reads.")
parser.add_argument('--min_cpg', help="The value of CpGs required per fragment (read pair combined number of CpGs). "
"default [1]",
default=1)
parser.add_argument('--out_dir', '-o', default='.')
parser.add_argument('--force', '-f', action='store_true', help='overwrite existing files if exists')
parser.add_argument('--debug', '-d', action='store_true')
parser.add_argument('--verbose', '-v', action='store_true')
parser.add_argument('-F', '--exclude_flags', type=int,
help='flags to exclude from bam file (samtools view parameter)',
default=None)
parser.add_argument('-q', '--mapq', type=int,
help=f'Minimal mapping quality (samtools view parameter)',
default=None)
add_GR_args(parser)
add_multi_thread_args(parser)
return parser
def parse_args():
parser = argparse.ArgumentParser(description=main.__doc__)
parser.add_argument('pat_files', nargs='+', help='Two or more pat files')
parser.add_argument(
'-c',
'--cov',
type=float,
help='Coverage of the output pat. '
'Default the coverage of the file with the highest rate. '
'Only supported if corresponding beta files are in the same '
'directory with the pat files. '
'Otherwise, they will be created.')
add_GR_args(parser)
parser.add_argument('-f',
'--force',
action='store_true',
help='Overwrite existing files if existed')
parser.add_argument('--reps',
type=int,
default=1,
help='nr or repetitions [1]')
parser.add_argument(
'--rates',
type=float,
metavar='[0.0, 1.0]',
nargs='+',
required=True,
help='Rates for each of the pat files. Note: the order matters!'
'Rate of for the last file may be omitted. '
'The rates will be adjusted s.t the output will be of the requested coverage.'
)
parser.add_argument('--labels',
nargs='+',
help='labels for the mixed reads. '
'Default is the basenames of the pat files,'
'lowercased and trimmed by the first "-"')
parser.add_argument(
'-L',
'--bed_file',
help='Only output reads overlapping the input BED FILE. ')
parser.add_argument(
'--strict',
action='store_true',
help='Truncate reads that start/end outside the given region. '
'Only relevant if "region", "sites" '
'or "bed_file" flags are given.')
out_or_pref = parser.add_mutually_exclusive_group()
out_or_pref.add_argument('-p', '--prefix', help='Prefix of output file.')
out_or_pref.add_argument('-o',
'--out_dir',
help='Output directory [.]',
default='.')
parser.add_argument(
'-@',
'--threads',
type=int,
default=multiprocessing.cpu_count(),
help='Number of threads to use (default: multiprocessing.cpu_count)')
args = parser.parse_args()
return args