def build_cob(args):
try:
# Build the refgen
refgen = co.RefGen(args.refgen)
# Check that the sep is likely right.
if len(pd.read_table(args.filename, sep=args.sep).columns) == 1:
print(("Detected only 1 column in {}, are you sure "
"colunms are separated by '{}'?").format(
args.filename, args.sep))
return None
if args.allow_non_membership:
refgen = refgen.copy('{}_tmp'.format(refgen.name),
'temp refgen'.format(refgen.name))
# Add non membership genes
for gid in pd.read_table(args.filename, sep=args.sep).index:
refgen.add_gene(Gene(None, None, id=gid))
quality_control = False if args.skip_quality_control else True
normalize = False if args.skip_normalization else True
quantile = False if args.skip_quantile else True
# Check to see if this dataset is already built
if available_datasets('Expr', args.name):
print('Warning! This dataset has already been built.')
co.Tools.del_dataset('Expr', args.name, force=args.force)
# Basically just pass all the CLI arguments to the COB class method
cob = co.COB.from_table(
args.filename,
args.name,
args.description,
refgen,
# Optional arguments
sep=args.sep,
rawtype=args.rawtype,
# Data Processing
quality_control=quality_control,
normalization=normalize,
quantile=quantile,
# Data processing parameters
max_gene_missing_data=args.max_gene_missing_data,
max_accession_missing_data=args.max_accession_missing_data,
min_single_sample_expr=args.min_single_sample_expr,
min_expr=args.min_expr,
max_val=args.max_val,
dry_run=args.dry_run,
zscore_cutoff=args.zscore_cutoff,
index_col=args.index_col)
print(cob.summary())
except Exception as e:
print("Build failed. Rolling back: removing corrupted files...")
co.Tools.del_dataset('Expr', args.name, force=True)
raise e
def build_gont(args):
refgen = co.RefGen(args.refgen)
# Check to see if this dataset is already built
if available_datasets('GOnt', args.name):
print('Warning! This dataset has already been built.')
co.Tools.del_dataset('GOnt', args.name, force=args.force)
go = co.GOnt.from_obo(args.obo_filename,
args.filename,
args.name,
args.description,
refgen,
go_col=args.go_col,
id_col=args.id_col)
print("Done: {}".format(go.summary()))
print('Build Successful')
def build_gont(args):
refgen = co.RefGen(args.refgen)
# Check to see if this dataset is already built
if available_datasets('GOnt',args.name):
print('Warning! This dataset has already been built.')
co.Tools.del_dataset('GOnt',args.name,force=args.force)
go = co.GOnt.from_obo(
args.obo_filename,
args.filename,
args.name,
args.description,
refgen,
go_col=args.go_col,
id_col=args.id_col,
headers=args.gene_term_header
)
print("Done: {}".format(go.summary()))
print('Build Successful')
def build_cob(args):
try:
# Build the refgen
refgen = co.RefGen(args.refgen)
# Check that the sep is likely right.
if len(pd.read_table(args.filename,sep=args.sep).columns) == 1:
print(
("Detected only 1 column in {}, are you sure "
"colunms are separated by '{}'?").format(args.filename,args.sep)
)
return None
elif len(pd.read_table(args.filename,sep=args.sep).columns) < 20 and args.non_interactive != True:
print(
("Detected fewer than 20 accessions in the expression matrix. "
"Calculating co-expression with this many datapoints is not advised")
)
if input('are you sure you want to continue? [y/n]: ').upper() == 'Y':
pass
else:
sys.exit(1)
if args.allow_non_membership:
refgen = refgen.copy(
'{}_tmp'.format(refgen.name),
'temp refgen'.format(refgen.name)
)
# Add non membership genes
for gid in pd.read_table(args.filename,sep=args.sep).index:
refgen.add_gene(Gene(None,None,id=gid))
quality_control = False if args.skip_quality_control else True
normalize = False if args.skip_normalization else True
quantile = False if args.skip_quantile else True
# Check to see if this dataset is already built
if available_datasets('Expr',args.name):
print('Warning! This dataset has already been built.')
co.Tools.del_dataset('Expr',args.name,force=args.force)
# Basically just pass all the CLI arguments to the COB class method
cob = co.COB.from_table(
args.filename,
args.name,
args.description,
refgen,
# Optional arguments
sep=args.sep,
rawtype=args.rawtype,
# Data Processing
quality_control=quality_control,
normalization=normalize,
quantile=quantile,
# Data processing parameters
max_gene_missing_data=args.max_gene_missing_data,
max_accession_missing_data=args.max_accession_missing_data,
min_single_sample_expr=args.min_single_sample_expr,
min_expr=args.min_expr,
max_val=args.max_val,
dry_run=args.dry_run,
zscore_cutoff=args.zscore_cutoff,
index_col=args.index_col
)
print(cob.summary())
except Exception as e:
print(f"Build failed for {args.name}. Rolling back: removing corrupted files...")
co.Tools.del_dataset('Expr',args.name,force=True)
raise e
def build_cob(args):
try:
# Build the refgen
refgen = co.RefGen(args.refgen)
# Check that the sep is likely right.
if len(pd.read_table(args.filename, sep=args.sep).columns) == 1:
print(("Detected only 1 column in {}, are you sure "
"colunms are separated by '{}'?").format(
args.filename, args.sep))
return None
elif (len(pd.read_table(args.filename, sep=args.sep).columns) < 20
and args.non_interactive != True):
print((
"Detected fewer than 20 accessions in the expression matrix. "
"Calculating co-expression with this many datapoints is not advised"
))
if input("are you sure you want to continue? [y/n]: ").upper(
) == "Y":
pass
else:
sys.exit(1)
if args.allow_non_membership:
refgen = refgen.copy("{}_tmp".format(refgen.name),
"temp refgen".format(refgen.name))
# Add non membership genes
for gid in pd.read_table(args.filename, sep=args.sep).index:
refgen.add_gene(Gene(None, None, id=gid))
quality_control = False if args.skip_quality_control else True
normalize = False if args.skip_normalization else True
quantile = True if args.quantile else False
# Check to see if this dataset is already built
if available_datasets("Expr", args.name):
print("Warning! This dataset has already been built.")
co.Tools.del_dataset("Expr", args.name, force=args.force)
# Basically just pass all the CLI arguments to the COB class method
cob = co.COB.from_table(
args.filename,
args.name,
args.description,
refgen,
# Optional arguments
sep=args.sep,
rawtype=args.rawtype,
# Data Processing
quality_control=quality_control,
normalization=normalize,
quantile=quantile,
# Data processing parameters
max_gene_missing_data=args.max_gene_missing_data,
max_accession_missing_data=args.max_accession_missing_data,
min_single_sample_expr=args.min_single_sample_expr,
min_expr=args.min_expr,
max_val=args.max_val,
dry_run=args.dry_run,
zscore_cutoff=args.zscore_cutoff,
index_col=args.index_col,
)
print(cob.summary())
except Exception as e:
print(
f"Build failed for {args.name}. Rolling back: removing corrupted files..."
)
co.Tools.del_dataset("Expr", args.name, force=True)
raise e
