def __init__(self,description=None,version=None):
"""Create a command line parser
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based
on the major command supplied at the start.
"""
self._name = os.path.basename(sys.argv[0])
self._description = description
self._version = version
self._commands = OrderedDictionary()
self._help = dict()
def __init__(self,title=None):
"""Create a new XLSWorkBook instance
Arguments:
title: optional, a title for the work book
"""
self.title = title
self.worksheet = OrderedDictionary()
def __init__(self, description=None, version=None, subparser=None):
"""Create a command line parser
with 'subparser' as the backend (default=OptionParser)
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based
on the major command supplied at the start.
"""
self._name = os.path.basename(sys.argv[0])
self._description = description
self._version = version
self._commands = OrderedDictionary()
self._help = dict()
if not subparser:
subparser = optparse.OptionParser
self._subparser = subparser
def __init__(self,description=None,version=None,subparser=None):
"""Create a command line parser
with 'subparser' as the backend (default=OptionParser)
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based
on the major command supplied at the start.
"""
self._name = os.path.basename(sys.argv[0])
self._description = description
self._version = version
self._commands = OrderedDictionary()
self._help = dict()
if not subparser:
subparser = optparse.OptionParser
self._subparser = subparser
class CommandParser:
"""Class defining multiple command line parsers
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based on the major
command ('CMD') supplied at the start of the line.
Usage:
Create a simple CommandParser using:
>>> p = CommandParser()
Add a 'setup' command:
>>> p.add_command('setup',usage='%prog setup OPTIONS ARGS')
Add options to the 'setup' command using normal OptionParser methods,
e.g.
>>> p.parser_for('info').add_option('-f',...)
To process a command line use the 'parse_args' method e.g.:
>>> cmd,options,args = p.parse_args()
The options and arguments can be accessed using the normal
methods from optparse.
"""
def __init__(self,description=None,version=None):
"""Create a command line parser
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based
on the major command supplied at the start.
"""
self._name = os.path.basename(sys.argv[0])
self._description = description
self._version = version
self._commands = OrderedDictionary()
self._help = dict()
def add_command(self,cmd,help=None,**args):
"""Add a major command to the CommandParser
Adds a command and creates an initial OptionParser
for it.
Arguments:
cmd: the command to be added
help: (optional) help text for the command
Other arguments are passed to the OptionParser object
when it is created i.e. 'usage', 'version',
'description'.
If 'version' isn't specified then the version
supplied to the CommandParser object will be used.
Returns:
OptionParser object for the command.
"""
if cmd in self._commands:
raise Exception("Command '%s' already defined" % cmd)
if 'version' not in args:
args['version'] = self._version
p = optparse.OptionParser(**args)
self._commands[cmd] = p
self._help[cmd] = help
return p
def parser_for(self,cmd):
"""Return optionparser for specified command
Returns:
The OptionParser object for the specified command.
"""
return self._commands[cmd]
def parse_args(self,argv=None):
"""Process a command line
Arguments:
argv: (optional) a list consisting of a command line.
If not supplied then defaults to sys.argv[1:].
Returns:
A tuple of (cmd,options,args) where 'cmd' is the
command, and 'options' and 'args' are the options and
arguments as returned by OptionParser.parse_args.
"""
# Collect arguments to process
if argv is None:
argv = sys.argv[1:]
if len(argv) == 0:
self.error("Need to supply a command\n%s" %
self.print_available_commands())
# Determine the major command and get the parser
cmd = argv[0]
self.handle_generic_commands(cmd)
try:
p = self.parser_for(cmd)
except KeyError:
# No parser
self.error("Usage: %s COMMAND [options] [args...]\n\n"
"%s: error: no such command: %s" %
(self._name,self._name,cmd))
# Parse the remaining arguments and return
options,arguments = p.parse_args(argv[1:])
return (cmd,options,arguments)
def error(self,message):
"""Exit with error message
"""
sys.stderr.write("%s\n" % message)
sys.exit(1)
def handle_generic_commands(self,cmd):
"""Process 'generic' commands e.g. 'help'
"""
if cmd in ('-h','--help','help'):
print "Usage: %s COMMAND [options] [args...]" % self._name
if self._description is not None:
print "\n%s" % self._description
print "%s" % self.print_available_commands()
sys.exit(0)
if cmd in ('--version'):
if self._version is not None:
version_str = self._version
print "%s" % version_str.replace('%prog',self._name)
sys.exit(0)
def list_commands(self):
"""Return the list of commands
"""
return self._commands.keys()
def print_available_commands(self):
"""Pretty-print available commands
Returns a 'pretty-printed' string for all options and commands,
with standard whitespace formatting.
"""
lines = ["\nOptions:"]
# Add generic commands
if self._version is not None:
lines.append(self.print_command("--version",
"show program's version number and exit"))
lines.append(self.print_command("-h, --help, help",
"show this help message and exit"))
# Add custom commands
lines.append("\nAvailable commands:")
for cmd in self.list_commands():
lines.append(self.print_command(cmd,self._help[cmd]))
lines.append("")
return '\n'.join(lines)
def print_command(self,cmd,message=None):
"""Print a line for a single command
Returns a 'pretty-printed' line for the specified command
and text, with standard whitespace formatting.
"""
text = [' ',cmd]
width = 22
if len(cmd) < width:
text.append(' '*(width-len(cmd)))
else:
text.append('\n '+' '*width)
if message is not None:
text.append(message)
return ''.join(text)
# Copyright (C) University of Manchester 2013-2018 Peter Briggs
#
########################################################################
#
# platforms.py
#
#########################################################################
"""platforms.py
Utilities and data to identify NGS sequencer platforms
"""
# Dictionary of sequencer platforms
from utils import OrderedDictionary
PLATFORMS = OrderedDictionary()
PLATFORMS['solid4'] = "SOLiD 4"
PLATFORMS['solid5500'] = "SOLiD 5500"
PLATFORMS['illumina-ga2x'] = "Illumina GAIIx"
PLATFORMS['hiseq4000'] = "Illumina HISeq 4000"
PLATFORMS['hiseq'] = "Illumina HISeq"
PLATFORMS['miseq'] = "Illumina MISeq"
PLATFORMS['miniseq'] = "MiniSeq"
PLATFORMS['nextseq'] = "Illumina NextSeq"
PLATFORMS['iseq'] = "Illumina iSeq"
PLATFORMS['other'] = "Unknown/external"
# Dictionary matching sequencing platforms to regexp patterns
# for specific instruments
SEQUENCERS = {
'^.*_ILLUMINA-73D9FA_.*$': 'illumina-ga2x',
class CommandParser(object):
"""Class defining multiple command line parsers
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based on the major
command ('CMD') supplied at the start of the line.
Usage:
Create a simple CommandParser which uses optparse.OptionParser as
the default subparser backend using:
>>> p = CommandParser()
Alternatively, specify argparse.ArgumentParser as the subparser
using:
>>> p = CommandParser(subparser=argparser.ArgumentParser)
Add a 'setup' command:
>>> p.add_command('setup',usage='%prog setup OPTIONS ARGS')
Add options to the 'setup' command using the appropriate methods
of the subparser (e.g. 'add_argument' for an
ArgumentParser instance).
For example:
>>> p.parser_for('info').add_argument('-f',...)
To process a command line, use the 'parse_args' method, for
example for an OptionParser-based subparser:
>>> cmd,options,args = p.parse_args()
Note that the exact form of the returned values depends on
on the subparser instance; it will be the same as that
returned by the 'parse_args' method of the subparser.
"""
def __init__(self, description=None, version=None, subparser=None):
"""Create a command line parser
with 'subparser' as the backend (default=OptionParser)
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based
on the major command supplied at the start.
"""
self._name = os.path.basename(sys.argv[0])
self._description = description
self._version = version
self._commands = OrderedDictionary()
self._help = dict()
if not subparser:
subparser = optparse.OptionParser
self._subparser = subparser
def add_command(self, cmd, help=None, **args):
"""Add a major command to the CommandParser
Adds a command, and creates and returns an initial
subparser instance for it.
Arguments:
cmd: the command to be added
help: (optional) help text for the command
Other arguments are passed to the subparser instance
when it is created i.e. 'usage', 'version',
'description'.
If 'version' isn't specified then the version
supplied to the CommandParser object will be used.
Returns:
Subparser instance object for the command.
"""
if cmd in self._commands:
raise Exception("Command '%s' already defined" % cmd)
if 'version' not in args:
args['version'] = self._version
p = self._subparser(**args)
self._commands[cmd] = p
self._help[cmd] = help
return p
def parser_for(self, cmd):
"""Return OptionParser for specified command
Returns:
The OptionParser object for the specified command.
"""
return self._commands[cmd]
def parse_args(self, argv=None):
"""Process a command line
Parses a command line (either those supplied to the calling
subprogram e.g. via the Python interpreter, or as a list).
Once the command is identified from the first argument, the
remainder of the arguments are passed to the 'parse_args'
method of the appropriate subparser for that command.
This method returns a tuple, with the first value being the
command, and the rest of the values being those returned
from the 'parse_args' method of the subparser.
Arguments:
argv: (optional) a list consisting of a command line.
If not supplied then defaults to sys.argv[1:].
Returns:
A tuple of (cmd,...), where 'cmd' is the command, and '...'
represents the values returned from the 'parse_args' method
of the subparser. For example, using the default OptionParser
backend returns (cmd,options,arguments), where 'options' and
'arguments' are the options and arguments as returned by
OptionParser.parse_args; using ArgumentParser as a backend
returns (cmd,arguments).
"""
# Collect arguments to process
if argv is None:
argv = sys.argv[1:]
if not argv:
self.error("Need to supply a command\n%s" %
self.print_available_commands())
# Determine the major command and get the parser
cmd = argv[0]
self.handle_generic_commands(cmd)
try:
p = self.parser_for(cmd)
except KeyError:
# No parser
self.error("Usage: %s COMMAND [options] [args...]\n\n"
"%s: error: no such command: %s" %
(self._name, self._name, cmd))
# Parse the remaining arguments and return
if isinstance(p, argparse.ArgumentParser):
options = p.parse_args(argv[1:])
return (cmd, options)
# else:
options, arguments = p.parse_args(argv[1:])
return (cmd, options, arguments)
def error(self, message):
"""Exit with error message
"""
sys.stderr.write("%s\n" % message)
sys.exit(1)
def handle_generic_commands(self, cmd):
"""Process 'generic' commands e.g. 'help'
"""
if cmd in ('-h', '--help', 'help'):
print "Usage: %s COMMAND [options] [args...]" % self._name
if self._description is not None:
print "\n%s" % self._description
print "%s" % self.print_available_commands()
sys.exit(0)
if cmd in ('--version', ):
if self._version is not None:
version_str = self._version
print "%s" % version_str.replace('%prog', self._name)
sys.exit(0)
def list_commands(self):
"""Return the list of commands
"""
return self._commands.keys()
def print_available_commands(self):
"""Pretty-print available commands
Returns a 'pretty-printed' string for all options and commands,
with standard whitespace formatting.
"""
lines = ["\nOptions:"]
# Add generic commands
if self._version is not None:
lines.append(
self.print_command("--version",
"show program's version number and exit"))
lines.append(
self.print_command("-h, --help, help",
"show this help message and exit"))
# Add custom commands
lines.append("\nAvailable commands:")
for cmd in self.list_commands():
lines.append(self.print_command(cmd, self._help[cmd]))
lines.append("")
return '\n'.join(lines)
def print_command(self, cmd, message=None):
"""Print a line for a single command
Returns a 'pretty-printed' line for the specified command
and text, with standard whitespace formatting.
"""
text = [' ', cmd]
width = 22
if len(cmd) < width:
text.append(' ' * (width - len(cmd)))
else:
text.append('\n ' + ' ' * width)
if message is not None:
text.append(message)
return ''.join(text)
class CommandParser(object):
"""Class defining multiple command line parsers
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based on the major
command ('CMD') supplied at the start of the line.
Usage:
Create a simple CommandParser which uses optparse.OptionParser as
the default subparser backend using:
>>> p = CommandParser()
Alternatively, specify argparse.ArgumentParser as the subparser
using:
>>> p = CommandParser(subparser=argparser.ArgumentParser)
Add a 'setup' command:
>>> p.add_command('setup',usage='%prog setup OPTIONS ARGS')
Add options to the 'setup' command using the appropriate methods
of the subparser (e.g. 'add_argument' for an
ArgumentParser instance).
For example:
>>> p.parser_for('info').add_argument('-f',...)
To process a command line, use the 'parse_args' method, for
example for an OptionParser-based subparser:
>>> cmd,options,args = p.parse_args()
Note that the exact form of the returned values depends on
on the subparser instance; it will be the same as that
returned by the 'parse_args' method of the subparser.
"""
def __init__(self,description=None,version=None,subparser=None):
"""Create a command line parser
with 'subparser' as the backend (default=OptionParser)
This parser can process command lines of the form
PROG CMD OPTIONS ARGS
where different sets of options can be defined based
on the major command supplied at the start.
"""
self._name = os.path.basename(sys.argv[0])
self._description = description
self._version = version
self._commands = OrderedDictionary()
self._help = dict()
if not subparser:
subparser = optparse.OptionParser
self._subparser = subparser
def add_command(self,cmd,help=None,**args):
"""Add a major command to the CommandParser
Adds a command, and creates and returns an initial
subparser instance for it.
Arguments:
cmd: the command to be added
help: (optional) help text for the command
Other arguments are passed to the subparser instance
when it is created i.e. 'usage', 'version',
'description'.
If 'version' isn't specified then the version
supplied to the CommandParser object will be used.
Returns:
Subparser instance object for the command.
"""
if cmd in self._commands:
raise Exception("Command '%s' already defined" % cmd)
if 'version' not in args:
args['version'] = self._version
p = self._subparser(**args)
self._commands[cmd] = p
self._help[cmd] = help
return p
def parser_for(self,cmd):
"""Return OptionParser for specified command
Returns:
The OptionParser object for the specified command.
"""
return self._commands[cmd]
def parse_args(self,argv=None):
"""Process a command line
Parses a command line (either those supplied to the calling
subprogram e.g. via the Python interpreter, or as a list).
Once the command is identified from the first argument, the
remainder of the arguments are passed to the 'parse_args'
method of the appropriate subparser for that command.
This method returns a tuple, with the first value being the
command, and the rest of the values being those returned
from the 'parse_args' method of the subparser.
Arguments:
argv: (optional) a list consisting of a command line.
If not supplied then defaults to sys.argv[1:].
Returns:
A tuple of (cmd,...), where 'cmd' is the command, and '...'
represents the values returned from the 'parse_args' method
of the subparser. For example, using the default OptionParser
backend returns (cmd,options,arguments), where 'options' and
'arguments' are the options and arguments as returned by
OptionParser.parse_args; using ArgumentParser as a backend
returns (cmd,arguments).
"""
# Collect arguments to process
if argv is None:
argv = sys.argv[1:]
if not argv:
self.error("Need to supply a command\n%s" %
self.print_available_commands())
# Determine the major command and get the parser
cmd = argv[0]
self.handle_generic_commands(cmd)
try:
p = self.parser_for(cmd)
except KeyError:
# No parser
self.error("Usage: %s COMMAND [options] [args...]\n\n"
"%s: error: no such command: %s" %
(self._name,self._name,cmd))
# Parse the remaining arguments and return
if isinstance(p,argparse.ArgumentParser):
options = p.parse_args(argv[1:])
return (cmd,options)
# else:
options,arguments = p.parse_args(argv[1:])
return (cmd,options,arguments)
def error(self,message):
"""Exit with error message
"""
sys.stderr.write("%s\n" % message)
sys.exit(1)
def handle_generic_commands(self,cmd):
"""Process 'generic' commands e.g. 'help'
"""
if cmd in ('-h','--help','help'):
print "Usage: %s COMMAND [options] [args...]" % self._name
if self._description is not None:
print "\n%s" % self._description
print "%s" % self.print_available_commands()
sys.exit(0)
if cmd in ('--version',):
if self._version is not None:
version_str = self._version
print "%s" % version_str.replace('%prog',self._name)
sys.exit(0)
def list_commands(self):
"""Return the list of commands
"""
return self._commands.keys()
def print_available_commands(self):
"""Pretty-print available commands
Returns a 'pretty-printed' string for all options and commands,
with standard whitespace formatting.
"""
lines = ["\nOptions:"]
# Add generic commands
if self._version is not None:
lines.append(self.print_command("--version",
"show program's version number and exit"))
lines.append(self.print_command("-h, --help, help",
"show this help message and exit"))
# Add custom commands
lines.append("\nAvailable commands:")
for cmd in self.list_commands():
lines.append(self.print_command(cmd,self._help[cmd]))
lines.append("")
return '\n'.join(lines)
def print_command(self,cmd,message=None):
"""Print a line for a single command
Returns a 'pretty-printed' line for the specified command
and text, with standard whitespace formatting.
"""
text = [' ',cmd]
width = 22
if len(cmd) < width:
text.append(' '*(width-len(cmd)))
else:
text.append('\n '+' '*width)
if message is not None:
text.append(message)
return ''.join(text)