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',
'--exon-numbering-key',
help="The name of the key containing the exon numbering.",
default="exon_nbr",
type=str)
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(
'-n',
'--no-check-gene-chr',
help=
"By default the command raise an error if several chromosomes are associated with the same gene_id. Disable this behaviour (but you should better think about what it means...).",
action="store_true")
return parser
def make_parser():
"""The program parser."""
parser = argparse.ArgumentParser(add_help=True)
parser.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.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="GTF",
type=arg_formatter.FormattedFile(mode='w',
file_ext=('gtf')))
parser.add_argument('-m',
'--min-exon-number',
help="Minimum number of exons.",
default=0,
type=int)
parser.add_argument('-M',
'--max-exon-number',
help="Maximum number of exons.",
default=None,
type=int)
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 (BED).",
default=sys.stdout,
metavar="BED",
type=arg_formatter.FormattedFile(mode='w',
file_ext='bed'))
parser_grp.add_argument('-c',
'--chrom-info',
help="Tabulated two-columns file. Chromosomes"
" as column 1 and their sizes as"
" column 2",
default=None,
metavar="CHROMINFO",
action=CheckChromFile,
required=True)
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="TXT",
type=arg_formatter.FormattedFile(mode='w',
file_ext='txt'))
parser_grp.add_argument(
'-s',
'--separator',
help="The separator to be used for separating key names.",
default="\n",
metavar="SEP",
type=str)
return parser
def make_parser():
"""parse"""
parser = argparse.ArgumentParser(add_help=True)
parser_grp = parser.add_argument_group('Argument')
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('-l', '--longs',
help="Take the longest transcript of each gene",
action="store_true")
parser_grp.add_argument('-g', '--keep-gene-lines',
help="Add gene lines to the output",
action="store_true")
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 FASTA file.",
default=sys.stdout,
metavar="FASTA",
type=arg_formatter.FormattedFile(mode='w', file_ext='fasta'))
parser_grp.add_argument('-g', '--genome',
help="The genome in fasta format.",
default=None,
metavar="FASTA",
required=True,
type=arg_formatter.FormattedFile(mode='r', file_ext='fasta'))
parser_grp.add_argument('-s', '--separator',
help="To separate info in header.",
default="|",
type=str,
required=False)
parser_grp.add_argument('-l', '--label',
help="A set of key for the header that will be extracted from the transcript line.",
default="feature,transcript_id,gene_id,seqid,start,end",
type=str,
required=False)
parser_grp.add_argument('-t', '--feature-type',
help="The feature type (one defined in column 3).",
type=str,
default="exon",
required=False)
parser_grp.add_argument('-n', '--no-rev-comp',
help="Don't reverse complement sequence "
"corresponding to gene on minus strand.",
action="store_true",
required=False)
parser_grp.add_argument('-r', '--rev-comp-to-header',
help="Indicate in the header whether sequence was rev-complemented.",
action="store_true",
required=False)
parser_grp.add_argument('-u', '--unique',
help="Don't write redondant IDS.",
action="store_true",
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('-i', '--inputfiles',
help="Complete paths to the OLOGRAM output text files",
type=arg_formatter.FormattedFile(mode='r', file_ext=('txt')),
nargs='+')
parser_grp.add_argument('-os', '--ori-shuffles',
help="How many shuffles were performed in the individual runs that will be merged?",
default=200,
type=int,
required=False)
parser_grp.add_argument('-o', '--output',
help="Destination path for the merged output file.",
default=None,
nargs=None,
type=arg_formatter.FormattedFile(mode='w', file_ext=('txt')),
required=True)
return parser
def make_parser():
"""The program parser."""
parser = argparse.ArgumentParser()
parser.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.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="GTF",
type=arg_formatter.FormattedFile(mode='w',
file_ext=('gtf')))
parser.add_argument('-g',
'--keep-gene-lines',
help="Add gene lines to the output",
action="store_true")
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",
required=False,
type=arg_formatter.FormattedFile(
mode='r', file_ext=('gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="TXT",
type=arg_formatter.FormattedFile(mode='w',
file_ext=('gtf')))
parser_grp.add_argument('-k',
'--key-name',
help="The name of the new key.",
default='tss_number',
type=str,
required=False)
parser_grp.add_argument(
'-c',
'--compute-dist',
help=
"Add a key indicating the distance to the first tss (the most 5').",
action='store_true')
parser_grp.add_argument(
'-d',
'--key-name-dist',
help="If --compute-dist is true a name for that key.",
default='dist_to_first_tss',
type=str,
required=False)
parser_grp.add_argument(
'-g',
'--add-nb-tss-to-gene',
help="Add the number of different tss to each gene",
action='store_true')
parser_grp.add_argument(
'-l',
'--gene-key',
help="The name of the key if --add-nb-tss-to-gene is selected.",
default='nb_tss',
type=str,
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",
required=False,
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('-a',
'--key-name',
type=str,
default="intron_sizes",
help="The name of the key.",
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 (BED).",
default=sys.stdout,
metavar="BED",
type=arg_formatter.FormattedFile(mode='w',
file_ext='bed'))
parser_grp.add_argument('-b',
'--by-transcript',
help="The intronic regions are returned for each"
" transcript.",
action="store_true")
parser_grp.add_argument(
'-n',
'--names',
help="The key(s) that should be used as name (if -b is used).",
default="gene_id,transcript_id",
metavar="NAME",
type=str)
parser_grp.add_argument(
'-s',
'--separator',
help=
"The separator to be used for separating name elements (if -b is used).",
default="|",
metavar="SEP",
type=str)
parser_grp.add_argument(
'-w',
'--intron-nb-in-name',
help=
"By default intron number is written in 'score' column. Force it to be written in 'name' column.",
action="store_true")
parser_grp.add_argument(
'-F',
'--no-feature-name',
help="Don't add the feature name ('intron') in the name column.",
action="store_true")
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 (BED).",
default=sys.stdout,
metavar="BED",
type=arg_formatter.FormattedFile(mode='w', file_ext='bed'))
parser_grp.add_argument('-t', '--ft-type',
help="The target feature (as found in the 3rd "
"column of the GTF).",
default='transcript',
type=str,
required=False)
parser_grp.add_argument('-v', '--invert',
help="Get 3' coordinate.",
action="store_true")
parser_grp.add_argument('-p', '--transpose',
help="Transpose coordinate in 5' (use negative value) or in 3' (use positive values).",
type=int,
required=False,
default=0)
parser_grp.add_argument('-n', '--names',
help="The key(s) that should be used as name.",
default="gene_id,transcript_id",
metavar="NAME",
type=str)
parser_grp.add_argument('-m', '--more-names',
help="A comma-separated list of information to be added to the 'name' column of the bed file.",
default=None,
type=str)
parser_grp.add_argument('-s', '--separator',
help="The separator to be used for separating name elements (see -n).",
default="|",
metavar="SEP",
type=str)
parser_grp.add_argument('-e', '--explicit',
help="Write explicitly the name of the keys in the header.",
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('-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('-s',
'--intron-size',
help="The minimum intron size.",
type=int,
default=100,
required=True)
parser_grp.add_argument(
'-m',
'--merged',
help=
"If selected, the sum of all intron lengths for a gene should be higher than s.",
action="store_true")
parser_grp.add_argument('-d',
'--delete-monoexonic',
help="Delete mono-exonic transcripts.",
action="store_true")
parser_grp.add_argument(
'-a',
'--add-intron-size',
help=
"Add a new key containing intron_size (comma-separated in order of apppearance) or the sum of intron size (see -m).",
action="store_true")
parser_grp.add_argument(
'-v',
'--invert-match',
help=
'Keep genes with an intron whose size is above s and delete others.',
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('-i',
'--inputfile',
help="Path to the GTF file. Default to STDIN.",
default=sys.stdin,
metavar="GTF",
required=False,
type=arg_formatter.FormattedFile(
mode='r', file_ext=('gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="BED/BED3/BED6",
type=arg_formatter.FormattedFile(mode='w',
file_ext='bed'))
parser_grp.add_argument('-n',
'--names',
help="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="The separator to be used for separating name elements (see -n).",
default="|",
metavar="SEP",
type=str)
parser_grp.add_argument(
'-m',
'--more-names',
help="Add this information to the 'name' column of the BED file.",
default="",
type=str)
parser_grp.add_argument('-f',
'--format',
help='Currently one of bed3, bed6',
type=str,
choices=('bed', 'bed3', 'bed6'),
default='bed6',
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="The tabulated file. Default to STDIN",
default=sys.stdin,
metavar="TXT",
type=arg_formatter.FormattedFile(mode='r',
file_ext='txt'))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="TXT",
type=arg_formatter.FormattedFile(mode='w',
file_ext='txt'))
parser_grp.add_argument('-c',
'--columns',
help="The list (csv) of column names.",
default=None,
type=str,
required=True)
parser_grp.add_argument('-n',
'--invert-match',
help='Not/invert match.',
action="store_true")
parser_grp.add_argument('-u',
'--unique',
help='Write non redondant lines.',
action="store_true")
parser_grp.add_argument(
'-s',
'--separator',
help="The separator to be used for separating name elements (see -n).",
default="\t",
metavar="SEP",
type=str)
parser_grp.add_argument('-H',
'--no-header',
help="Don't print the header line.",
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('-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 name of the attribute for which a "
"prefix/suffix is to be added to the corresponding"
" values (e.g, gene_id, transcript_id...).",
default="chrom",
metavar="KEY",
type=str)
parser_grp.add_argument(
'-t',
'--text',
help='The character string to add as a prefix to the values.',
default="chr",
metavar="TEXT",
type=str)
parser_grp.add_argument(
'-s',
'--suffix',
help='The character string to add as a prefix to the values.',
action="store_true",
required=False)
parser_grp.add_argument('-f',
'--target-feature',
help='The name of the target feature.',
default="*",
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('-c',
'--chrom-info',
help="Tabulated two-columns file. Chromosomes"
" as column 1 and sizes as"
" column 2 ",
default=None,
metavar="CHROMINFO",
action=CheckChromFile,
required=True)
parser_grp.add_argument(
'-u',
'--upstream',
help="Extends the tts in 5' by a given value (int)."
" Defines the region around the tts.",
default=1500,
metavar="UPSTREAM",
type=int,
required=False)
parser_grp.add_argument(
'-d',
'--downstream',
help="Extends the region in 3' by a given value (int)."
" Defines the region around the tts.",
default=1500,
metavar="DOWNSTREAM",
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(
'-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 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='comma-separated list of keys to join.',
default=None,
metavar="KEY",
type=str,
required=True)
parser_grp.add_argument('-d',
'--dest-key',
help='The target key name.',
default=None,
metavar="KEY",
type=str,
required=True)
parser_grp.add_argument('-s',
'--separator',
help="The separator for the concatenated values.",
default="|",
metavar="SEP",
type=str)
parser_grp.add_argument('-f',
'--target-feature',
help='The name of the target feature.',
default="*",
type=str,
required=False)
return parser
def make_parser():
"""The program CLI."""
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('-s',
'--shift-value',
help="Shift coordinate by s nucleotides.",
default=0,
type=int,
required=True)
parser_grp.add_argument('-d',
'--stranded',
help="By default shift not .",
action="store_true")
parser_grp.add_argument(
'-a',
'--allow-outside',
help=
"Accept the partial or total disappearance of a feature upon shifting.",
action="store_true")
parser_grp.add_argument('-c',
'--chrom-info',
help="Tabulated two-columns file. Chromosomes"
" as column 1 and sizes as"
" column 2 ",
default=None,
metavar="CHROMINFO",
action=CheckChromFile,
required=True)
return parser
def make_parser():
"""The program parser."""
parser = argparse.ArgumentParser(add_help=True)
parser.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.add_argument('-o', '--outputfile',
help="Output file.",
default=sys.stdout,
metavar="GTF",
type=arg_formatter.FormattedFile(mode='w', file_ext=('gtf')))
parser.add_argument('-g', '--go-id',
help='The GO ID (with or without "GO:" prefix).',
default="GO:0003700",
type=str,
required=False)
parser_mut = parser.add_mutually_exclusive_group(required=True)
parser_mut.add_argument('-l', '--list-datasets',
help='Do not select lines. Only get a list of available datasets/species.',
action="store_true",
required=False)
parser_mut.add_argument('-s', '--species',
help='The dataset/species.',
default=None,
type=str,
required=False)
parser.add_argument('-n', '--invert-match',
help='Not/invert match.',
action="store_true")
parser.add_argument('-p1', '--http-proxy',
help='Use this http proxy (not tested/experimental).',
default='',
type=str,
required=False)
parser.add_argument('-p2', '--https-proxy',
help='Use this https proxy (not tested/experimental).',
default='',
type=str,
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="TXT",
type=arg_formatter.FormattedFile(mode='w',
file_ext='txt'))
parser_grp.add_argument('-k',
'--key-name',
help="The comma separated list of key name.",
default=None,
type=str,
required=True)
parser_grp.add_argument('-s',
'--separator',
help="The separator used if -c or -p are true.",
default="\t",
type=str,
required=False)
parser_grp.add_argument(
'-c',
'--count',
help=
"Add the counts for each key (separator will be set to '\t' by default).",
action="store_true")
parser_grp.add_argument(
'-p',
'--print-key-name',
help="Also print the key name in the first column.",
action="store_true")
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('-i',
'--inputfile',
help="Complete path to the OLOGRAM output file",
type=arg_formatter.FormattedFile(mode='r',
file_ext=('tsv')),
required=True)
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',
'--query-label',
help="Name of the query for display",
default="Query",
type=str,
required=False)
parser_grp.add_argument(
'-t',
'--top-s',
help=
"Optional. Only the top t combinations sorted by total basepairs in real data will be displayed.",
default=-1,
type=int,
required=False)
parser_grp.add_argument(
'-mh',
'--min_inheritance',
help=
"Optional. A combination will be added to a shorter parent in the tree only if it represents at least a proportion MH of its true base pairs (between 0 and 1).",
default=-1,
type=float,
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',
'--key-to-join',
help='The name of the key used to join (e.g transcript_id).',
default=None,
metavar="KEY",
type=str,
required=True)
parser_grp.add_argument(
'-t',
'--target-feature',
help='The name(s) of the target feature(s). Comma-separated.',
default=None,
type=str,
required=False)
parser_grp.add_argument(
'-m',
'--matrix-files',
help="A set of matrix files with row names as "
"target keys column names as novel key and each cell as value.",
type=argparse.FileType('r'),
nargs='+')
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 CEAS file.",
default=None,
type=argparse.FileType('r'),
required=True)
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
type=arg_formatter.FormattedFile(mode='w',
file_ext='gtf'))
parser_grp.add_argument('-t',
'--target-table',
help="The target table.",
default="GeneTable",
type=str,
required=False)
parser_grp.add_argument('-s',
'--show-tables',
help="Only list tables and exit.",
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('-s', '--species-name',
help="The species name.",
type=str,
metavar="SPECIES",
default="homo_sapiens",
required=False)
parser_grp.add_argument('-o', '--outputfile',
help="Output file (gtf.gz).",
metavar="GTF.GZ",
type=arg_formatter.FormattedFile(mode='w', file_ext='gtf.gz'))
parser_grp.add_argument('-e', '--ensembl-collection',
help="Which ensembl collection to interrogate"
"('vertebrate', 'protists', 'fungi', 'plants', 'metazoa').",
default="vertebrate",
choices=[
'vertebrate',
'protists',
'fungi',
'plants',
'metazoa'],
type=str)
parser_grp.add_argument('-r', '--release',
help="Release number. By default, the latest.",
default=None,
metavar="RELEASE",
type=str)
parser_grp.add_argument('-l', '--list-only',
help="If selected, list available species.",
action='store_true',
required=False)
parser_grp.add_argument('-hs', '--hide-species-name',
help="If selected, hide species names upon listing.",
action='store_true',
required=False)
parser_grp.add_argument('-c', '--to-stdout',
help='This option specifies that output will go to '
'the standard output stream, leaving downloaded'
' files intact (or not, see -d).',
action='store_true',
required=False)
parser_grp.add_argument('-d', '--delete',
help='Delete the gtf file after processing (e.g if -c is used).',
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('-i',
'--inputfile',
help="Path to the GTF file. Default to STDIN",
default=sys.stdin,
metavar="GTF/BED",
type=arg_formatter.FormattedFile(
mode='r', file_ext=('bed', 'gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file (BED).",
default=sys.stdout,
metavar="BED",
type=arg_formatter.FormattedFile(mode='w',
file_ext='bed'))
parser_grp.add_argument('-t',
'--ft-type',
help="The target feature (as found in the 3rd "
"column of the GTF).",
default='transcript',
type=str,
required=False)
parser_grp.add_argument('-n',
'--names',
help="The key(s) that should be used as name.",
default="transcript_id",
metavar="NAME",
type=str)
parser_grp.add_argument(
'-s',
'--separator',
help="The separator to be used for separating name elements (see -n).",
default="|",
metavar="SEP",
type=str)
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 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",
required=False,
type=arg_formatter.FormattedFile(
mode='r', file_ext=('gtf', 'gtf.gz')))
parser_grp.add_argument('-o',
'--outputfile',
help="Output file.",
default=sys.stdout,
metavar="TXT",
type=arg_formatter.FormattedFile(mode='w',
file_ext='txt'))
parser_grp.add_argument('-k',
'--keys',
default="*",
help="The set of keys of interest.",
type=str,
required=False)
parser_grp.add_argument(
'-t',
'--additional-text',
help="A facultative text to be printed in the third "
"column (e.g species name).",
default=None,
metavar="TEXT",
type=str,
required=False)
parser_grp.add_argument('-u',
'--uniq',
help="Ask for the count of non redondant values.",
action="store_true",
required=False)
return parser
