def log(msg=None, addextrastick=True):
if addextrastick:
msg = op.msgformated(msg, withnewline=False)
printOnConsole = True
with open(glob.logfile, mode='a+') as f:
if msg is not None:
f.write(msg)
f.write('\n')
if printOnConsole:
print(msg)
def main(args=None):
if args is None:
args = sys.argv[1:]
# Parse arguments
headertxt = op.topline()
headertxt += op.msgformated(
'Clust\n'
'Optimised consensus clustering of multiple heterogeneous datasets\n'
'Version {0}\n'
'\n'
'By Basel Abu-Jamous\n'
'Department of Plant Sciences\n'
'The University of Oxford\n'
'*****@*****.**'.format(version), '^')
headertxt += op.midline()
headertxt += op.msgformated('Citation\n' '~~~~~~~~', '^')
citationtxt = 'When publishing work that uses Clust, please cite:\n' \
'Basel Abu-Jamous and Steven Kelly (2018) Clust: automatic extraction of optimal co-expressed ' \
'gene clusters from gene expression data. Genome Biology 19:172; ' \
'doi: https://doi.org/10.1186/s13059-018-1536-8.'
# TODO: citation
headertxt += op.msgformated(citationtxt, '<')
headertxt += op.midline()
headertxt += op.msgformated(
'Full description of usage can be found at:\n'
'https://github.com/BaselAbujamous/clust', '<')
headertxt += op.bottomline()
parser = argparse.ArgumentParser(description=headertxt,
formatter_class=RawTextHelpFormatter)
parser.add_argument('datapath',
help='Data file path or directory with data file(s).',
default=None)
parser.add_argument(
'-n',
metavar='<file or int>',
help='Normalisation file or list of codes (default: 1000)',
default=['1000'],
nargs='+')
parser.add_argument('-r',
metavar='<file>',
help='Replicates structure file',
default=None)
parser.add_argument('-m',
metavar='<file>',
help='OrthoGroups (OGs) mapping file',
default=None)
parser.add_argument('-o',
metavar='<directory>',
help='Output directory',
default=None)
parser.add_argument('-t',
metavar='<real number>',
type=float,
help='Cluster tightness (default: 1.0).',
default=1.0)
parser.add_argument(
'-basemethods',
metavar='<string>',
nargs='+',
help='One or more base clustering methods (default: k-means)',
default=None)
parser.add_argument(
'-K',
metavar='<integer>',
type=int,
nargs='+',
help='K values, e.g. 2 4 6 10 ... (default: 4 to 20 (step=4))',
default=[n for n in range(4, 21, 4)])
parser.add_argument('-s',
metavar='<real number>',
type=float,
help='Outlier standard deviations (default: 3.0)',
default=3.0)
parser.add_argument(
'-d',
metavar='<integer>',
type=int,
help='Min datasets in which a gene must exist (default: 1)',
default=1)
parser.add_argument(
'-fil-v',
metavar='<real number>',
dest='filv',
type=float,
help='Filtering: gene expression threshold (default: -inf)',
default=-float("inf"))
parser.add_argument('-fil-c',
metavar='<integer>',
dest='filc',
type=int,
help='Filtering: number of conditions (default: 0)',
default=0)
parser.add_argument('-fil-d',
metavar='<integer>',
dest='fild',
type=int,
help='Filtering: number of datasets (default: 1)',
default=0)
parser.add_argument('--fil-abs',
dest='absval',
action='store_true',
help='Filter using absolute values of expression')
parser.add_argument(
'--fil-perc',
dest='filperc',
action='store_true',
help='-fil-v is a percentile of genes rather than raw value')
parser.add_argument(
'--fil-flat',
dest='filflat',
action='store_true',
help='Filter out genes with flat expression profiles (default)')
parser.add_argument('--no-fil-flat',
dest='filflat',
action='store_false',
help='Cancels the default --fil-flat option')
parser.add_argument('-cs',
metavar='<integer>',
type=int,
help='Smallest cluster size (default: 11)',
default=11)
parser.add_argument('-q3s',
metavar='<real number>',
type=float,
help='Q3'
's defining outliers (default: 2.0)',
default=2.0)
parser.add_argument('--no-optimisation',
dest='optimisation',
action='store_false',
help='Skip cluster optimsation & completion')
parser.add_argument(
'--deterministic',
dest='deterministic',
action='store_true',
help='Obsolete. All steps are already deterministic (v1.7.4+)')
parser.add_argument('-np',
metavar='<integer>',
type=int,
help='Number of parallel processes (default: 1)',
default=1)
parser.set_defaults(optimisation=True,
deterministic=False,
absval=False,
filperc=False,
filflat=True)
# parser.add_argument('-ec', type=int, help='Perform error correction, 1 or 0 (default: 1)', default=1)
if len(args) == 0:
parser.parse_args(['-h'])
args = parser.parse_args(args)
if args.filperc:
filtype = 'perc'
else:
filtype = 'raw'
if args.basemethods is not None:
args.basemethods = [[m] for m in args.basemethods]
# Call the clust function
clustpipeline.clustpipeline(args.datapath, args.m, args.r, args.n, args.o,
args.K, args.t, args.s, args.d, args.filv,
args.filc, args.fild, args.absval, filtype,
args.filflat, args.cs, args.np,
args.optimisation, args.q3s, args.basemethods,
args.deterministic)
