def make_parser():
"""The parser."""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Arguments')
parser_grp.add_argument('-i',
'--inputfile',
help="Path to the GTF file. Default to STDIN",
default=sys.stdin,
metavar="GTF",
type=arg_formatter.FormattedFile(
mode='r', file_ext=('gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="GTF",
type=arg_formatter.FormattedFile(mode='w',
file_ext=('gtf')))
parser_grp.add_argument(
'-n',
'--number',
help="The number of transcripts or gene to select.",
default=1,
metavar="NUMBER",
type=arg_formatter.ranged_num(lowest=1,
highest=None,
linc=True,
val_type='int'),
required=False)
parser_grp.add_argument('-t',
'--ft-type',
help="The type of feature.",
default="transcript",
choices=["gene", "transcript"],
required=False)
parser_grp.add_argument('-s',
'--seed-value',
help="Seed value for the random number generator.",
default=None,
metavar="SEED",
type=arg_formatter.ranged_num(lowest=1,
highest=None,
linc=True,
val_type='int'),
required=False)
return parser
def make_parser():
"""The parser."""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Arguments')
parser_grp.add_argument('-i',
'--inputfile',
help="Path to the GTF file. Default to STDIN",
default=sys.stdin,
metavar="GTF",
type=arg_formatter.FormattedFile(
mode='r', file_ext=('gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="GTF",
type=arg_formatter.FormattedFile(mode='w',
file_ext=('gtf')))
parser_grp.add_argument(
'-m',
'--max-transcript',
help="The maximum number of transcripts to select for each gene.",
default=1,
metavar="MAX",
type=arg_formatter.ranged_num(lowest=1,
highest=None,
linc=True,
val_type='int'),
required=False)
parser_grp.add_argument('-s',
'--seed-value',
help="Seed value for the random number generator.",
default=None,
metavar="SEED",
type=arg_formatter.ranged_num(lowest=1,
highest=None,
linc=True,
val_type='int'),
required=False)
return parser
def make_parser():
"""The main argument parser."""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Arguments')
parser_grp.add_argument('inputfiles',
help="Complete paths to the OLOGRAM output files",
type=arg_formatter.FormattedFile(mode='r',
file_ext=('txt')),
nargs='+')
parser_grp.add_argument('-pw',
'--pdf-width',
help='Output pdf file width (inches).',
type=arg_formatter.ranged_num(0, None),
default=None,
required=False)
parser_grp.add_argument('-ph',
'--pdf-height',
help='Output pdf file height (inches).',
type=arg_formatter.ranged_num(0, None),
default=None,
required=False)
parser_grp.add_argument('-o',
'--output',
help="Pdf file name.",
default=None,
nargs=None,
type=arg_formatter.FormattedFile(mode='w',
file_ext='pdf'),
required=True)
parser_grp.add_argument('-l',
'--labels',
help="A comma separated list of labels.",
default=None,
type=str,
required=False)
return parser
def make_parser():
"""The program parser."""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Arguments')
parser_grp.add_argument('-i',
'--inputfile',
help="Path to the GTF file. Default to STDIN",
default=sys.stdin,
metavar="GTF",
type=arg_formatter.FormattedFile(
mode='r', file_ext=('gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="GTF",
type=arg_formatter.FormattedFile(mode='w',
file_ext=('gtf')))
parser_grp.add_argument('-k',
'--src-key',
help='The name of the source key',
default=None,
type=str,
required=True)
parser_grp.add_argument('-d',
'--dest-key',
help='The name of the target key.',
default=None,
type=str,
required=True)
parser_grp.add_argument('-n',
'--nb-levels',
help='The number of levels/classes to create.',
default=2,
metavar="KEY",
type=arg_formatter.ranged_num(lowest=1,
highest=None,
linc=True,
val_type='int'),
required=True)
parser_grp.add_argument(
'-l',
'--labels',
help="A comma-separated list of labels of size --nb-levels.",
default=None,
type=str,
required=False)
parser_grp.add_argument(
'-p',
'--percentiles',
help="Compute --nb-levels classes using percentiles.",
action="store_true",
required=False)
parser_grp.add_argument('-g',
'--log',
help="Compute breaks based on log-scale.",
action="store_true",
required=False)
parser_grp.add_argument(
'-u',
'--percentiles-of-uniq',
help="Compute percentiles based on non-redondant values.",
action="store_true",
required=False)
parser_grp.add_argument('-r',
'--precision',
help="The precision used in naming intervals.",
type=int,
default=2,
required=False)
return parser
def make_parser():
"""The main parser."""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Arguments')
parser_grp.add_argument('-i',
'--inputfile',
help="A GTF file or bed file. A GTF if <stdin>.",
default=sys.stdin,
metavar="GTF/BED",
type=arg_formatter.FormattedFile(
mode='r', file_ext=('bed', 'gtf', 'gtf.gz')))
parser_grp.add_argument('-y',
'--bigwiglist',
help='A list of Bigwig files (last argument).',
type=arg_formatter.FormattedFile(
mode='r', file_ext='bigwig'),
nargs='+',
required=True)
parser_grp.add_argument(
'-o',
'--outputfile',
help="Output file name (.zip extension will be added).",
default=sys.stdout,
metavar="GTF/TXT",
required=True,
type=argparse.FileType('w'))
parser_grp.add_argument('-l',
'--labels',
help='Bigwig labels (i.e short name version for '
'plotting).',
default=None,
type=str,
required=False)
parser_grp.add_argument('-t',
'--ft-type',
help='If input is a GTF, the region to analyse.',
default='promoter',
choices=[
'promoter', 'tts', 'transcript',
'user_regions', 'single_nuc'
],
type=str,
required=False)
parser_grp.add_argument('-p',
'--pseudo-count',
help='Pseudo-count to add to all values.',
default=0,
type=arg_formatter.ranged_num(lowest=0,
highest=None,
val_type="float",
linc=True),
required=False)
parser_grp.add_argument(
'-u',
'--upstream',
help="Extend the region of interest in 5' by a given value.",
default=1000,
type=arg_formatter.ranged_num(lowest=0,
highest=None,
val_type="int",
linc=True),
required=False)
parser_grp.add_argument(
'-d',
'--downstream',
help="Extend the region of interest in 3' by a given value.",
default=1000,
type=arg_formatter.ranged_num(lowest=0,
highest=None,
val_type="int",
linc=True),
required=False)
parser_grp.add_argument('-c',
'--chrom-info',
help='Tabulated file (chr as '
'column 1, sizes as column 2.)',
default=None,
action=CheckChromFile,
required=True)
parser_grp.add_argument('-w',
'--bin-nb',
help='Split the region into w bins.',
default=100,
type=arg_formatter.ranged_num(lowest=1,
highest=None,
val_type="int",
linc=True),
required=False)
parser_grp.add_argument('-k',
'--nb-proc',
help='Use this many threads to compute coverage.',
default=1,
type=arg_formatter.ranged_num(lowest=1,
highest=None,
val_type="int",
linc=True),
required=False)
parser_grp.add_argument('-b',
'--bin-around-frac',
help="Fraction of bins used in 5' and 3' regions.",
default=0.1,
type=float,
required=False)
parser_grp.add_argument(
'-zn',
'--zero-to-na',
help='Use NA not zero when region is undefined in bigwig.',
action='store_true',
required=False)
parser_grp.add_argument(
'-nst',
'--no-stranded',
help='The bins should not be oriented relative to strand.',
action='store_true',
required=False)
return parser
def add_command(cls, cmd):
""" Add new argument parser for a command. Note that
verbosity, keep-temp and help arguments are added by default."""
# ----------------------------------------------------------------------
# Command help display
# ----------------------------------------------------------------------
cmd_desc_list = re.split('\n[ \t]*\n', cmd.desc)
cmd_desc_str = " Description: "
for i in cmd_desc_list:
cmd_desc_str += "\n\n " + textwrap.fill(
textwrap.dedent(left_strip_str(i)).strip(),
100,
initial_indent=' ',
subsequent_indent=' ')
cmd.desc = cmd_desc_str
if cmd.notes is not None:
cmd.notes = cmd.notes.lstrip("\n")
cmd.notes = cmd.notes.strip()
cmd.notes = cmd.notes.strip("--")
cmd.notes = cmd.notes.strip(" ")
tokens = cmd.notes.split("--")
cmd.desc += "\n\n" + textwrap.fill(
textwrap.dedent("Notes:").strip(),
100,
initial_indent=' ',
subsequent_indent=' ')
for i in range(len(tokens)):
cmd.desc += "\n" + textwrap.fill(
textwrap.dedent(" * " +
left_strip_str(tokens[i].strip())).strip(),
100,
initial_indent=' ',
subsequent_indent=' ')
if cmd.references is not None:
cmd.references = cmd.references.lstrip("\n")
cmd.references = cmd.references.strip()
cmd.references = cmd.references.strip("--")
cmd.references = cmd.references.strip(" ")
tokens = cmd.references.split("--")
cmd.desc += "\n\n" + textwrap.fill(
textwrap.dedent("References:").strip(),
100,
initial_indent=' ',
subsequent_indent=' ')
for i in range(len(tokens)):
cmd.desc += "\n" + textwrap.fill(
textwrap.dedent(" * " +
left_strip_str(tokens[i].strip())).strip(),
100,
initial_indent=' ',
subsequent_indent=' ')
cmd.desc = re.sub("\-\\\-", "--", cmd.desc)
# ----------------------------------------------------------------------
# Define command-wise args
# ----------------------------------------------------------------------
if cmd.lang == "Python":
group = cmd.parser.add_argument_group(
'Command-wise optional arguments')
# help is a default argument for any command
group.add_argument("-h",
"--help",
action="help",
help="Show this help message and exit.")
# verbose is a default argument of any command
group.add_argument("-V",
"--verbosity",
default=0,
type=ranged_num(lowest=0,
highest=3,
val_type="int",
linc=True,
hinc=True),
help="Set output verbosity ([0-3]).",
nargs='?',
required=False)
# verbose is a default argument of any command
group.add_argument("-D",
"--no-date",
action="store_true",
help="Do not add date to output file names.")
# verbose is a default argument of any command
group.add_argument(
"-C",
"--add-chr",
action="store_true",
help="Add 'chr' to chromosome names before printing output.")
# keep-temp-file is a default argument of any command
group.add_argument("-K",
"--tmp-dir",
type=str,
default=None,
help="Keep all temporary files into this folder.",
required=False)
# keep-temp-file is a default argument of any command
group.add_argument(
"-A",
"--keep-all",
action="store_true",
help=
"Try to keep all temporary files even if process does not terminate normally.",
required=False)
# logger-file can be used to store the requested command
# arguments into a file.
group.add_argument(
"-L",
"--logger-file",
type=str,
help='Stores the arguments passed to the command into a file.',
required=False)
# logger-file can be used to store the requested command
# arguments into a file.
group.add_argument("-W",
"--write-message-to-file",
type=argparse.FileType('w'),
default=None,
help='Store all message into a file.',
required=False)
# Add the command to the list of known command
cls.cmd_obj_list[cmd.name] = cmd
# Update the global argument parser
arg_dict = {
'name': cmd.name,
'formatter_class': ArgFormatter,
'parents': [cmd.parser],
'help': cmd.message,
'add_help': False,
'description': cmd.desc
}
if cmd.group == 'editing':
cls.grp_editing.add_parser(**arg_dict)
elif cmd.group == 'information':
cls.grp_info.add_parser(**arg_dict)
elif cmd.group == 'selection':
cls.grp_select.add_parser(**arg_dict)
elif cmd.group == 'conversion':
cls.grp_convert.add_parser(**arg_dict)
elif cmd.group == 'coordinates':
cls.grp_coord.add_parser(**arg_dict)
elif cmd.group == 'annotation':
cls.grp_annot.add_parser(**arg_dict)
elif cmd.group == 'ologram':
cls.grp_ologram.add_parser(**arg_dict)
elif cmd.group == 'sequences':
cls.grp_seq.add_parser(**arg_dict)
elif cmd.group == 'coverage':
cls.grp_cov.add_parser(**arg_dict)
elif cmd.group == 'miscellaneous':
cls.grp_misc.add_parser(**arg_dict)
else:
raise ValueError("Unknow group for command : %s" % cmd.name)
def make_parser():
"""The program parser."""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Arguments')
parser_mut = parser.add_mutually_exclusive_group(required=False)
parser_grp.add_argument('-i',
'--inputfile',
help="Path to the GTF file. Default to STDIN",
default=sys.stdin,
metavar="GTF",
type=arg_formatter.FormattedFile(
mode='r', file_ext=('gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="GTF",
type=arg_formatter.FormattedFile(mode='w',
file_ext=('gtf')))
parser_grp.add_argument('-k',
'--key',
help='The key name.',
default=None,
metavar="KEY",
type=str,
required=False)
parser_mut.add_argument('-v',
'--value',
help='A comma-separated list of values.',
default=None,
metavar="VALUE",
type=str)
parser_mut.add_argument(
'-f',
'--file-with-values',
help='A file containing values as a single column.',
default=None,
metavar="FILE",
type=argparse.FileType("r"))
parser_grp.add_argument(
'-c',
'--col',
help=
'The column number (one-based) that contains the values in the file. File is tab-delimited.',
default=1,
metavar="COL",
type=arg_formatter.ranged_num(lowest=1,
highest=None,
linc=True,
val_type='int'),
required=False)
parser_grp.add_argument(
'-n',
'--invert-match',
help=
'Not/invert match. Select lines whose selected key is not associated'
' with the selected values.',
action="store_true")
parser_grp.add_argument('-b',
'--bed-format',
help='Ask for bed format output.',
action="store_true")
parser_grp.add_argument(
'-m',
'--names',
help="If Bed output. The key(s) that should be used as name.",
default="gene_id,transcript_id",
metavar="NAME",
type=str)
parser_grp.add_argument(
'-s',
'--separator',
help=
"If Bed output. The separator to be used for separating name elements (see -n).",
default="|",
metavar="SEP",
type=str)
parser_grp.add_argument(
'-l',
'--log',
help=
'Print some statistics about selected features. To be used in conjunction with -V 1/2.',
action="store_true",
required=False)
parser_mut.add_argument('-t',
'--select-transcripts',
help='A shortcuts for "-k feature -v transcript".',
action="store_true",
required=False)
parser_mut.add_argument('-g',
'--select-genes',
help='A shortcuts for "-k feature -v gene".',
action="store_true",
required=False)
parser_mut.add_argument('-e',
'--select-exons',
help='A shortcuts for "-k feature -v exon".',
action="store_true",
required=False)
parser_mut.add_argument('-d',
'--select-cds',
help='A shortcuts for "-k feature -v CDS".',
action="store_true",
required=False)
parser_mut.add_argument(
'-a',
'--select-start-codon',
help='A shortcuts for "-k feature -v start_codon".',
action="store_true",
required=False)
return parser
def make_parser():
"""The program parser."""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Arguments')
parser_grp.add_argument('--in-file', '-i',
metavar='TXT',
help='A two columns tab-file. See notes.',
default=None,
type=arg_formatter.FormattedFile(mode='r', file_ext='txt'),
required=True)
parser_grp.add_argument('--reference-gene-file', '-r',
metavar='TXT',
help='The file containing the reference gene list (1 column,'
' transcript ids).'
' No header.',
default=None,
type=arg_formatter.FormattedFile(mode='r', file_ext='txt'),
required=True)
parser_grp.add_argument('--out-dir', '-o',
help='Name of the output directory.',
type=str,
metavar='DIR',
default="control_list",
required=False)
parser_grp.add_argument('--log2', '-l',
help='If selected, data will be log transformed.',
action="store_true",
required=False)
parser_grp.add_argument('--pseudo-count', '-p',
help='The value for a pseudo-count to be added.',
type=float,
default=0,
required=False)
parser_grp.add_argument('-pw', '--page-width',
help='Output pdf file width (e.g. 7 inches).',
type=arg_formatter.ranged_num(lowest=0,
highest=None,
linc=False,
val_type='float'),
default=None,
required=False)
parser_grp.add_argument('-ph', '--page-height',
help='Output file height (e.g. 5 inches).',
type=arg_formatter.ranged_num(lowest=0,
highest=None,
linc=False,
val_type='float'),
default=None,
required=False)
parser_grp.add_argument('-pf', '--page-format',
help='Output file format.',
choices=['pdf', 'png'],
default='pdf',
required=False)
parser_grp.add_argument('-dpi', '--dpi',
help='Dpi to use.',
type=arg_formatter.ranged_num(lowest=0,
highest=None,
linc=False,
val_type='int'),
default=300,
required=False)
parser_grp.add_argument('--skip-first', '-s',
help='Indicates that infile hase a header.',
action="store_true",
required=False)
parser_grp.add_argument('--rug', '-u',
help='Add rugs to the diagram.',
action="store_true",
required=False)
parser_grp.add_argument('--jitter', '-j',
help='Add jittered points.',
action="store_true",
required=False)
parser_grp.add_argument('-if', '--user-img-file',
help="Provide an alternative path for the image.",
default=None,
type=argparse.FileType("w"),
required=False)
parser_grp.add_argument('-c', '--set-colors',
help='Colors for the two sets (comma-separated).',
default="#b2df8a,#6a3d9a",
type=str,
required=False)
return parser_grp