def getUI(prog_name, args):
longDescription = "..."
shortDescription = longDescription
ui = CLI(prog_name, shortDescription, longDescription)
ui.minArgs = 2
ui.maxArgs = 2
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output resultant reads to these files",
required=False,
type=str))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run.",
required=False))
ui.addOption(
Option(short="h", long="help", description="show this help message "))
ui.addOption(Option(short="u", long="test", description="run unit tests "))
ui.parseCommandLine(args)
return ui
def getUI_lookup_index(prog_name, args):
"""
build and return a UI object for the 'build' option.
:param args: raw arguments to parse
"""
programName = prog_name
long_description = "Build an index for one or more files."
short_description = long_description
ui = CLI(programName, short_description, long_description)
ui.minArgs = 2
ui.maxArgs = 2
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output to given file, else stdout",
required=False,
type=str))
ui.addOption(
Option(short="k",
long="key",
argName="key",
description="the key to lookup; if missing, the " +
"program runs in interactive mode. ",
required=False,
type=str))
ui.addOption(
Option(short="t",
long="type",
argName="filename",
description="the type of the file. If missing, " +
"the script will try to guess the file type. " +
"Supported file types are: " +
", ".join([f.name for f in FileType]),
required=False,
type=str))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run (default: " + str(DEFAULT_VERBOSITY) + ")",
default=DEFAULT_VERBOSITY,
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(prog_name, args):
longDescription = "Given two files consisting of mapped reads, remove " +\
"the reads that are in both mapped in exonic regions " +\
"and junction regions "
shortDescription = "Filter ambigious reads"
ui = CLI(prog_name, shortDescription, longDescription)
ui.minArgs = -1
ui.maxArgs = -1
ui.addOption(
Option(short="f",
long="first",
argName="filename",
description="BED file with first end reads",
required=True,
type=str))
ui.addOption(
Option(short="s",
long="second",
argName="filename",
description="BED file with second end reads",
required=True,
type=str))
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="whitespace separated list of output" +
" filenames, wrap in commas. Expect two" +
" filenames here, one for each input.",
required=True,
type=str))
ui.addOption(
Option(short="v",
long="verbose",
description="outputs additional messages to stdout " +
"about run (default: " + str(DEFAULT_VERBOSITY) + ")",
default=DEFAULT_VERBOSITY,
required=False))
ui.addOption(
Option(short="b",
long="best",
description="keep clearly " + "better ambiguously mapped reads",
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(args):
"""
build and return a UI object for this script.
:param args: raw arguments to parse
"""
programName = os.path.basename(sys.argv[0])
longDescription = "takes a file with a list of p-values and applies " +\
"Benjamini and Hochberg FDR to convert to q-values "
shortDescription = "takes a file with a list of p-values and applies " +\
"Benjamini and Hochberg FDR to convert to q-values "
ui = CLI(programName, shortDescription, longDescription)
ui.minArgs = 0
ui.maxArgs = 1
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output to given file, else stdout",
required=False,
type=str))
ui.addOption(
Option(short="f",
long="field",
argName="number",
description="the field that contains the p-values " +
"(indexed from 1, as with unix 'cut' " + "command)",
default=4,
required=False,
type=int))
ui.addOption(
Option(short="e",
long="header",
description="take the first line as a header ",
default=False,
required=False))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run (default: " + str(DEFAULT_VERBOSITY) + ")",
default=DEFAULT_VERBOSITY,
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(prog_name, args):
"""Build and return user interface object for this script."""
longDescription = "Given a set of BED intervals, pile them up so that " +\
"their start positions are aligned and then count the " +\
"number of other regions that overlap them."
shortDescription = longDescription
ui = CLI(prog_name, shortDescription, longDescription)
# gotta have two args -- MAF dir/file and BED regions.
# Input by stdin not allowed
ui.minArgs = 2
ui.maxArgs = 2
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output to given file, else stdout",
required=False,
type=str))
ui.addOption(
Option(short="a",
long="anchor",
argName="anchor-point",
description="5-prime, start",
required=False,
type=str))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run",
required=False))
ui.addOption(
Option(short="n",
long="normalize",
description="normalize counts by number of regions " +
"overlapping that position",
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(args):
"""
build and return a UI object for this script.
:param args: raw arguments to parse
"""
programName = os.path.basename(sys.argv[0])
longDescription = "takes a file with a list of p-values and applies " +\
"Benjamini and Hochberg FDR to convert to q-values "
shortDescription = "takes a file with a list of p-values and applies " +\
"Benjamini and Hochberg FDR to convert to q-values "
ui = CLI(programName, shortDescription, longDescription)
ui.minArgs = 2
ui.maxArgs = 2
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output to given file, else stdout",
required=False,
type=str))
ui.addOption(
Option(short="s",
long="stranded",
description="treat regions on separate strands as " +
"disjoint, even if they overlap",
required=False))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run",
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(args):
"""
build and return a UI object for this script.
:param args: raw arguments to parse
"""
programName = os.path.basename(sys.argv[0])
longDescription = "Compute the Jaccard index for two sets of genomic " +\
"intervals."
shortDescription = longDescription
ui = CLI(programName, shortDescription, longDescription)
ui.minArgs = 2
ui.maxArgs = 2
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run",
required=False))
ui.addOption(
Option(short="s",
long="stranded",
description="treat regions on separate strands as " +
"disjoint, even if they overlap",
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(prog_name, args):
longDescription = "Convert junction reads into exonic reads by picking " +\
"an exon to assign them to"
shortDescription = longDescription
ui = CLI(prog_name, shortDescription, longDescription)
ui.minArgs = 0
ui.maxArgs = 1
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output resultant reads to these files",
required=False,
type=str))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run (default: " + str(DEFAULT_VERBOSITY) + ")",
default=DEFAULT_VERBOSITY,
required=False))
ui.addOption(
Option(short="s",
long="scheme",
argName="TYPE",
description="scheme for assigning reads to " +
"junctions, one of FIRST_EXON, " +
"SECOND_EXON, BOTH_EXONS, BIGGEST_EXON",
default=DEFAULT_SCHEME,
required=False,
type=str))
ui.addOption(
Option(short="h", long="help", description="show this help message "))
ui.addOption(Option(short="u", long="test", description="run unit tests "))
ui.parseCommandLine(args)
return ui
def getUI(prog_name, args):
longDescription = "compute the nucleotide frequency at each position in " +\
"a fastq file"
shortDescription = longDescription
ui = CLI(prog_name, shortDescription, longDescription)
ui.minArgs = 1
ui.maxArgs = 1
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output resultant table to this file. " +
"If omitted, output is to stdout",
required=False,
type=str))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="v",
long="verbose",
description="outputs additional messages to stdout " +
"about run (default: " + str(DEFAULT_VERBOSITY) + ")",
default=DEFAULT_VERBOSITY,
required=False))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(prog_name, args):
"""Build and return user interface object for this script."""
longDescription = "Given a set of BED intervals, compute a profile of " +\
"conservation by averaging over all intervals using a " +\
"whole genome alignment to a set of relevent species." +\
"\n\n" +\
"Usage: " + prog_name + " [options] regions.bed " +\
"genome-alig species" +\
"\n\n" +\
"genome-alig can be either a single MAF file, or a " +\
"directory of MAF files. In the latter case, the " +\
"directory may also optionally contain index files for " +\
"the alignment files."
shortDescription = longDescription
ui = CLI(prog_name, shortDescription, longDescription)
# gotta have two args -- MAF dir/file and BED regions.
# Input by stdin not allowed
ui.minArgs = 3
ui.maxArgs = 4
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output to given file, else stdout",
required=False,
type=str))
ui.addOption(
Option(short="w",
long="window",
argName="size",
description="size of window to compute around each " +
"interval; " + str(DEFAULT_WINDOW_SIZE) +
" to use whole interval. " + "Default " +
str(DEFAULT_WINDOW_SIZE),
required=False,
type=int))
ui.addOption(
Option(short="e",
long="extensions",
argName="extension",
description="if genome-alig specifies a directory, " +
"treat files with this extension as " + "alignment files.",
required=False,
type=str))
ui.addOption(
Option(short="i",
long="index-extensions",
argName="extension",
description="if genome-alig specifies a directory, " +
"treat files with this extension as " +
"index files for alignments.",
required=False,
type=str))
ui.addOption(
Option(short="f",
long="fail-no-index",
description="fail if an alignment file without an " +
"index is found; otherwise index-less " +
"alignment files are loaded whole (which " +
"might be slow if they're large, and " +
"might require a lot of memory)",
default=False,
required=False))
ui.addOption(
Option(short="m",
long="missing",
argName="strategy",
description="how to treat missing sequences in " +
"blocks. Options are " +
", ".join([str(x.name) for x in MissingSequenceHandler]),
required=False,
type=str))
ui.addOption(
Option(short="s",
long="species",
argName="species",
description="consider only these species. Default is " + "all.",
required=False,
type=str))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run (default: " + str(DEFAULT_VERBOSITY) + ")",
default=DEFAULT_VERBOSITY,
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui
def getUI(args, prog_name):
"""
build and return a UI object for this script.
:param args: raw arguments to parse
"""
longDescription = "Collapse the regions in a file of genomic intervals "
shortDescription = longDescription
ui = CLI(prog_name, shortDescription, longDescription)
ui.minArgs = 1
ui.maxArgs = 1
ui.addOption(
Option(short="o",
long="output",
argName="filename",
description="output to given file, else stdout",
required=False,
type=str))
ui.addOption(
Option(short="s",
long="stranded",
description="collapse positive and negative " +
"strands independently (otherwise strand " +
"is ignored and all output regions are on " + "positive strand",
default=False,
required=False))
ui.addOption(
Option(short="a",
long="accumulate_names",
description="accumulate names of the regions, " +
"separated by semi-colon (otherwise " +
"all output region names will be 'X').",
default=False,
required=False))
ui.addOption(
Option(short="e",
long="exact",
description="collapse only regions with exactly the " +
" same genomic location (otherwise any " +
"overlapping regions are collapsed)",
default=False,
required=False))
ui.addOption(
Option(short="v",
long="verbose",
description="output additional messages to stderr " +
"about run (default: " + str(DEFAULT_VERBOSITY) + ")",
default=DEFAULT_VERBOSITY,
required=False))
ui.addOption(
Option(short="h",
long="help",
description="show this help message ",
special=True))
ui.addOption(
Option(short="u",
long="test",
description="run unit tests ",
special=True))
ui.parseCommandLine(args)
return ui