def run(self):
parser = create_parser(self.description, self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.target),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.target))
parser.add_argument(get_arg_name_from_enum(ArgDesc.bamfile),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.bamfile))
parser.add_argument(get_arg_name_from_enum(ArgDesc.region),
type=str,
help=get_arg_help_from_enum(ArgDesc.region))
parser.add_argument(get_arg_name_from_enum(ArgDesc.no_parallel),
dest=ArgDesc.no_parallel.name,
action='store_true',
default=False,
help=get_arg_help_from_enum(
ArgDesc.no_parallel))
args = parse_sub_command(parser)
parallel = not getattr_by(ArgDesc.no_parallel, args)
NRR(bedfile=getattr_by(ArgDesc.target, args),
bamfile=getattr_by(ArgDesc.bamfile, args),
region=getattr_by(ArgDesc.region, args),
parallel=parallel,
to_label=False)
def run(self):
parser = create_parser(self.description, command=self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.target),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.target))
parser.add_argument(get_arg_name_from_enum(ArgDesc.spacing),
type=int,
default=20,
help=get_arg_help_from_enum(ArgDesc.spacing))
parser.add_argument(get_arg_name_from_enum(ArgDesc.min_data),
type=int,
default=50,
help=get_arg_help_from_enum(ArgDesc.min_data))
parser.add_argument(get_arg_name_from_enum(ArgDesc.max_pool),
type=int,
default=None,
help=get_arg_help_from_enum(ArgDesc.max_pool))
parser.add_argument(get_arg_name_from_enum(ArgDesc.output),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.output))
args = parse_sub_command(parser)
roi = ROI(getattr_by(ArgDesc.target, args),
spacing=getattr_by(ArgDesc.spacing, args),
mindata=getattr_by(ArgDesc.min_data, args),
maxpool=getattr_by(ArgDesc.max_pool, args))
bedwrite(getattr_by(ArgDesc.output, args),
roi.targets,
header=False)
def run(self):
parser = create_parser(self.description, command=self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.cfg_file),
type=str,
required=True,
help=get_arg_name_from_enum(ArgDesc.cfg_file))
args = parse_sub_command(parser)
CNVConfig(getattr_by(ArgDesc.cfg_file, args))
def run(self):
parser = create_parser(self.description, command=self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.vcf),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.vcf))
parser.add_argument(get_arg_name_from_enum(ArgDesc.output),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.output))
args = parse_sub_command(parser)
vcf = VCF(getattr_by(ArgDesc.vcf, args))
df = vcf.variants.drop(columns=['info'])
bedwrite(getattr_by(ArgDesc.output, args), df)
def __init__(self):
self.__nrr_comparator = None
self.__vcf_comparator = None
commands = [
command.lower() for command in dir(self) if command[0].isupper()
]
self.instances = defaultdict(lambda: None)
available_commands = ''
for command in commands:
try:
# create instance of "command" classes
self.instances[command] = getattr(self,
command.capitalize())(self)
available_commands += '''
{}
\t{}
'''.format(self.instances[command].name,
self.instances[command].description)
except AttributeError:
sys.exit(
Strings.wrong_command.value.format(command,
self._Command.__name__))
parser = create_parser(Strings.description.value,
usage='''{}
{}
{}
{}'''.format(Strings.usage.value.format(Strings.command.value),
Strings.available_commands.value, available_commands,
Strings.getting_help.value))
parser.add_argument(Strings.command.value,
help=Strings.command_help.value)
args = parser.parse_args(sys.argv[1:2])
if not hasattr(self, args.command.capitalize()):
sys.exit(Strings.unrecognized_command.value.format(args.command))
self.instances[args.command].run()
def run(self):
parser = create_parser(self.description, command=self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.no_rd),
dest=ArgDesc.no_rd.name,
action='store_true',
default=False,
help=get_arg_help_from_enum(ArgDesc.no_rd))
parser.add_argument(get_arg_name_from_enum(ArgDesc.no_vcf),
dest=ArgDesc.no_vcf.name,
action='store_true',
default=False,
help=get_arg_help_from_enum(ArgDesc.no_vcf))
parser.add_argument(get_arg_name_from_enum(ArgDesc.outdir),
type=str,
default=Strings.default_outdir.value,
help=get_arg_help_from_enum(ArgDesc.outdir))
args = parse_sub_command(parser)
ratio = not getattr_by(ArgDesc.no_rd, args)
variant = not getattr_by(ArgDesc.no_vcf, args)
nrrtest = self.outer_instance.get_instance_by_name(
self.outer_instance.nrr_comparator).run() if ratio else None
vcftest = self.outer_instance.get_instance_by_name(
self.outer_instance.vcf_comparator).run() if ratio else None
cnvtest = CNVTest(nrrtest,
vcftest,
path=getattr_by(ArgDesc.outdir, args))
cnvtest.analyze_plot()
rfname = '{}/cnvfrombam.csv'.format(cnvtest.path2table)
vfname = '{}/cnvfromvcf.csv'.format(cnvtest.path2table)
if ratio:
cnvtest.blocks[0].to_csv(rfname, sep='\t', index=False)
if variant:
cnvtest.blocks[-1].to_csv(vfname, sep='\t', index=False)
cnvtest.save()
cnvtest.summary()
print('Done!')
def run(self):
parser = create_parser(self.description, command=self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.file),
type=str,
help=get_arg_help_from_enum(ArgDesc.file))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.chroms),
nargs='+',
type=str,
default=[
'chr%s' % i for i in list(range(1, 23)) + ['M', 'X', 'Y']
],
help=get_arg_help_from_enum(ArgDesc.chroms))
parser.add_argument(get_arg_name_from_enum(ArgDesc.chrom_height),
type=float,
default=1,
help=get_arg_help_from_enum(
ArgDesc.chrom_height))
parser.add_argument(get_arg_name_from_enum(ArgDesc.chrom_spacing),
type=float,
default=1.5,
help=get_arg_help_from_enum(
ArgDesc.chrom_spacing))
parser.add_argument(get_arg_name_from_enum(ArgDesc.fig_size),
type=float,
nargs=2,
default=None,
help=get_arg_help_from_enum(ArgDesc.fig_size))
parser.add_argument(get_arg_name_from_enum(ArgDesc.legend),
nargs=2,
action='append',
default=None,
help=get_arg_help_from_enum(ArgDesc.legend))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.above_track_file),
type=str,
help='{}. {}'.format(
Strings.ideo_track_file.value,
get_arg_help_from_enum(ArgDesc.above_track_file)))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.above_track_height),
type=float,
default=0.5,
help=get_arg_help_from_enum(Strings.ideo_track_height))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.above_track_padding),
type=float,
default=0.6,
help=get_arg_help_from_enum(ArgDesc.above_track_padding))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.above_track_color),
type=str,
default='#0ab26c',
help=get_arg_help_from_enum(ArgDesc.above_track_color))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.above_track_alpha),
type=float,
default=0.5,
help=get_arg_help_from_enum(ArgDesc.above_track_alpha))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.above_track_linewidths),
help=get_arg_help_from_enum(ArgDesc.above_track_linewidths))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.below_track_file),
type=str,
help='{}. {}'.format(
Strings.ideo_track_file.value,
get_arg_help_from_enum(ArgDesc.below_track_file)))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.below_track_height),
type=float,
default=-0.5,
help=get_arg_help_from_enum(Strings.ideo_track_height))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.below_track_padding),
type=float,
default=-0.1,
help=get_arg_help_from_enum(ArgDesc.below_track_padding))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.below_track_color),
type=str,
default='#cc1231',
help=get_arg_help_from_enum(ArgDesc.below_track_color))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.below_track_alpha),
type=float,
default=0.5,
help=get_arg_help_from_enum(ArgDesc.below_track_alpha))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.below_track_linewidths),
help=get_arg_help_from_enum(ArgDesc.below_track_linewidths))
parser.add_argument(get_arg_name_from_enum(ArgDesc.output),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.output))
args = parse_sub_command(parser)
# load chromosomes
fig_size = getattr_by(ArgDesc.fig_size, args)
fig_size = tuple(fig_size) if fig_size is not None else fig_size
ideo = Ideogram(file=getattr_by(ArgDesc.file, args),
chroms=getattr_by(ArgDesc.chroms, args),
chrom_height=getattr_by(ArgDesc.chrom_height,
args),
chrom_spacing=getattr_by(ArgDesc.chrom_spacing,
args),
fig_size=fig_size)
# add data above
above_file = getattr_by(ArgDesc.above_track_file, args)
if above_file is not None:
ideo.add_data(
load_table(getattr_by(ArgDesc.above_track_file, args)),
height=getattr_by(ArgDesc.above_track_height, args),
padding=getattr_by(ArgDesc.above_track_padding, args),
color=getattr_by(ArgDesc.above_track_color, args),
alpha=getattr_by(ArgDesc.above_track_alpha, args),
linewidths=getattr_by(ArgDesc.above_track_linewidths,
args))
# add data below
above_file = getattr_by(ArgDesc.below_track_file, args)
if above_file is not None:
ideo.add_data(
load_table(getattr_by(ArgDesc.below_track_file, args)),
height=getattr_by(ArgDesc.below_track_height, args),
padding=getattr_by(ArgDesc.below_track_padding, args),
color=getattr_by(ArgDesc.below_track_color, args),
alpha=getattr_by(ArgDesc.below_track_alpha, args),
linewidths=getattr_by(ArgDesc.below_track_linewidths,
args))
legend = getattr_by(ArgDesc.legend, args)
if legend is not None:
ideo.add_legend(parse_legend(legend))
ideo.save(getattr_by(ArgDesc.output, args))
def run(self) -> VCFTest:
parser = create_parser(self.description, self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.vcf_baseline),
required=True,
action='append',
nargs='?',
help=get_arg_help_from_enum(
ArgDesc.vcf_baseline))
parser.add_argument(get_arg_name_from_enum(ArgDesc.vcf_test),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.vcf_test))
parser.add_argument(get_arg_name_from_enum(ArgDesc.vcf_metric),
type=str,
default='IQR',
choices={'std', 'IQR'},
help=get_arg_help_from_enum(
ArgDesc.vcf_metric))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.vcf_interval_range),
type=float,
default=1.5,
help=get_arg_help_from_enum(ArgDesc.vcf_interval_range))
parser.add_argument(get_arg_name_from_enum(ArgDesc.vcf_size),
type=int,
default=400,
help=get_arg_help_from_enum(ArgDesc.vcf_size))
parser.add_argument(get_arg_name_from_enum(ArgDesc.vcf_step),
type=int,
default=40,
help=get_arg_help_from_enum(ArgDesc.vcf_step))
parser.add_argument(
get_arg_name_from_enum(ArgDesc.vcf_cnv_like_range),
type=float,
default=0.7,
help=get_arg_help_from_enum(ArgDesc.vcf_cnv_like_range))
parser.add_argument(get_arg_name_from_enum(ArgDesc.vcf_max_dist),
type=int,
default=15000000,
help=get_arg_help_from_enum(
ArgDesc.vcf_max_dist))
parser.add_argument(get_arg_name_from_enum(ArgDesc.to_filter),
dest=ArgDesc.to_filter.name,
action='store_true',
default=True,
help=get_arg_help_from_enum(ArgDesc.to_filter))
parser.add_argument(get_arg_name_from_enum(ArgDesc.outdir),
type=str,
default=Strings.default_outdir.value,
help=get_arg_help_from_enum(ArgDesc.outdir))
args = parse_sub_command(parser)
sample = VCF(getattr_by(ArgDesc.vcf_test, args))
baseline = VCFList(getattr_by(ArgDesc.vcf_baseline, args))
vcftest = VCFTest(
baseline,
sample,
metric=getattr_by(ArgDesc.vcf_metric, args),
interval_range=getattr_by(ArgDesc.vcf_interval_range, args),
size=getattr_by(ArgDesc.vcf_size, args),
step=getattr_by(ArgDesc.vcf_step, args),
cnv_like_range=getattr_by(ArgDesc.vcf_cnv_like_range, args),
maxdist=getattr_by(ArgDesc.vcf_max_dist, args),
path=getattr_by(ArgDesc.outdir, args))
if getattr_by(ArgDesc.to_filter, args):
vcftest.filter()
vcftest.load_filtered_out()
if vcftest.filtered_out_pos is None:
vcftest.compare()
vcftest.save_filtered_out()
vcftest.eliminate_vars()
vcftest.split()
print('Creating plots at {}'.format(vcftest.path2plot))
vcftest.vcfplot()
filename = '{}/vcftest.csv'.format(vcftest.path2table)
print('Writing table at {}'.format(filename))
vcftest.df.to_csv(filename, sep='\t', index=False)
print('Done!')
return vcftest
def run(self) -> NRRTest:
parser = create_parser(self.description, command=self.name)
parser.add_argument(get_arg_name_from_enum(ArgDesc.baseline),
required=True,
action='append',
nargs='?',
help=get_arg_help_from_enum(ArgDesc.baseline))
parser.add_argument(get_arg_name_from_enum(ArgDesc.test),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.test))
parser.add_argument(get_arg_name_from_enum(ArgDesc.target),
type=str,
required=True,
help=get_arg_help_from_enum(ArgDesc.target))
parser.add_argument(get_arg_name_from_enum(ArgDesc.size),
type=int,
default=200,
help=get_arg_help_from_enum(ArgDesc.size))
parser.add_argument(get_arg_name_from_enum(ArgDesc.step),
type=int,
default=10,
help=get_arg_help_from_enum(ArgDesc.step))
parser.add_argument(get_arg_name_from_enum(ArgDesc.metric),
type=str,
default='IQR',
choices={'std', 'IQR'},
help=get_arg_help_from_enum(ArgDesc.metric))
parser.add_argument(get_arg_name_from_enum(ArgDesc.interval_range),
type=float,
default=1.5,
help=get_arg_help_from_enum(
ArgDesc.interval_range))
parser.add_argument(get_arg_name_from_enum(ArgDesc.min_read),
type=int,
default=30,
help=get_arg_help_from_enum(ArgDesc.min_read))
parser.add_argument(get_arg_name_from_enum(ArgDesc.below_cutoff),
type=float,
default=0.7,
help=get_arg_help_from_enum(
ArgDesc.below_cutoff))
parser.add_argument(get_arg_name_from_enum(ArgDesc.above_cutoff),
type=float,
default=1.3,
help=get_arg_help_from_enum(
ArgDesc.above_cutoff))
parser.add_argument(get_arg_name_from_enum(ArgDesc.max_dist),
type=int,
default=15000000,
help=get_arg_help_from_enum(ArgDesc.max_dist))
parser.add_argument(get_arg_name_from_enum(ArgDesc.cnv_like_range),
type=float,
default=0.7,
help=get_arg_help_from_enum(
ArgDesc.cnv_like_range))
parser.add_argument(get_arg_name_from_enum(ArgDesc.bins),
type=int,
default=500,
help=get_arg_help_from_enum(ArgDesc.bins))
parser.add_argument(get_arg_name_from_enum(ArgDesc.method),
type=str,
default='chr_group',
choices={'chr_group'})
parser.add_argument(get_arg_name_from_enum(ArgDesc.outdir),
type=str,
default=Strings.default_outdir.value,
help=get_arg_help_from_enum(ArgDesc.outdir))
args = parse_sub_command(parser)
# load amplicons and define targets
roi = ROI(getattr_by(ArgDesc.target, args))
# load test sample and count number of reads in regions of targets
sample = NRR(bamfile=getattr_by(ArgDesc.test, args), bed=roi)
# load baseline samples and count their number of reads in region of targets
baseline = NRRList(bamfiles=getattr_by(ArgDesc.baseline, args),
bed=roi)
# make test
nrrtest = NRRTest(
baseline,
sample,
path=getattr_by(ArgDesc.outdir, args),
size=getattr_by(ArgDesc.size, args),
step=getattr_by(ArgDesc.step, args),
metric=getattr_by(ArgDesc.metric, args),
interval_range=getattr_by(ArgDesc.interval_range, args),
minread=getattr_by(ArgDesc.min_read, args),
below_cutoff=getattr_by(ArgDesc.below_cutoff, args),
above_cutoff=getattr_by(ArgDesc.above_cutoff, args),
maxdist=getattr_by(ArgDesc.max_dist, args),
cnv_like_range=getattr_by(ArgDesc.cnv_like_range, args),
bins=getattr_by(ArgDesc.bins, args),
method=getattr_by(ArgDesc.method, args))
nrrtest.make_ratio()
if nrrtest.ratios:
print('Creating plots at {}'.format(nrrtest.path2plot))
nrrtest.plot()
filename = '{}/nrrtest.csv'.format(nrrtest.path2table)
print('Writing table at {}'.format(filename))
nrrtest.df.to_csv(filename, sep='\t', index=False)
print('Done!')
return nrrtest
