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):
"""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, 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
# 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',
