def ipa_ureg_validation(ipa_ureg_parameters):
ureg_types_dict = {}
# iterates for each supplied ureg parameter:
for ureg_parameter in ipa_ureg_parameters:
# required inputs
ureg_file_path = None
type = None
# gets the sub-parameters
sub_params_list = ureg_parameter.split(",")
# checks the sub params
for sub_param in sub_params_list:
# Tests if there are two parts to the sub-parameter
if len(sub_param.split("=")) != 2:
print >> sys.stderr, "Error: the ipa_ureg parameter: " + ureg_parameter + " is not in the correct format (missing =)."
sys.exit(1)
# Tests the file sub-parameter
if sub_param.upper().startswith("file=".upper()):
ureg_file_path = sub_param.split("=")[1]
# Tests if the gene set file can be opened:
try:
ureg_file = open(ureg_file_path).readlines()
except:
print >> sys.stderr, "Error: the ureg file: " + ureg_file_path + " cannot be opened."
sys.exit(1)
# Tests if the gene set file is in the correct format:
line_counter = 0
for line in ureg_file:
line_split = line.rstrip().split("\t")
if len(line_split) != 3:
print >> sys.stderr, "Error: the ureg file: " + ureg_file_path + " line " + str(
line_counter) + "does not have exactly 3 columns."
sys.exit(1)
# Tests the type sub-parameter
if sub_param.upper().startswith("type=".upper()):
type = sub_param.split("=")[1].upper()
# Tests the zscore sub-parameter
if sub_param.upper().startswith("zscore=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (zscore)."
sys.exit(1)
# Tests the p.adj sub-parameter
if sub_param.upper().startswith("p.adj=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (p.adj)."
sys.exit(1)
# Tests the log2fold sub-parameter
if sub_param.upper().startswith("log2fold=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (log2fold)."
sys.exit(1)
# Tests the min set size sub-parameter
if sub_param.upper().startswith("min_set_size=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (min_set_size)."
sys.exit(1)
# Tests the max set size sub-parameter
if sub_param.upper().startswith("max_set_size=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (max_set_size)."
sys.exit(1)
# Tests the overlap ratio sub-parameter
if sub_param.upper().startswith("network_overlap_ratio=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (network_overlap_ratio)."
sys.exit(1)
# Tests the overlap size sub-parameter
if sub_param.upper().startswith("network_overlap_size=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (network_overlap_size)."
sys.exit(1)
# Checks for a unique gene sets type:
if type in ureg_types_dict:
print >> sys.stderr, "Error: the ipa_ureg parameter: " + ureg_parameter + " has does not have a unique type."
sys.exit(1)
else:
ureg_types_dict[type] = True
# tests if the required inputs have been supplied
if ureg_file_path == None or type == None:
print >> sys.stderr, "Error: the hypergeom_gs parameter: " + ureg_parameter + " is not in the correct format (missing essential sub-parameters)."
sys.exit(1)
print "validated the ipa_ureg parameter: " + ureg_parameter
def pde_parsing(pde_workflow_parameters, global_variables):
parsed_pde_parameters = []
for pde_parameter in pde_workflow_parameters:
# default sub-parameters
pde_file_path = None
numerator_group = None
denominator_group = None
p_threshold = 0.05
fold_threshold = 1
order_list = None
gl_file_path = None
# gets the sub-parameters
sub_params_list = pde_parameter.split(",")
for sub_param in sub_params_list:
if sub_param.upper().startswith("file=".upper()):
pde_file_path = sub_param.split("=")[1]
if sub_param.upper().startswith("numerator=".upper()):
numerator_group = sub_param.split("=")[1].upper()
if sub_param.upper().startswith("denominator=".upper()):
denominator_group = sub_param.split("=")[1].upper()
if sub_param.upper().startswith("p.adj=".upper()):
p_threshold = float(sub_param.split("=")[1])
if sub_param.upper().startswith("log2fold=".upper()):
fold_threshold = float(sub_param.split("=")[1])
if sub_param.upper().startswith("order=".upper()):
order_list = sub_param.split("=")[1].split("+")
order_list = [x.upper() for x in order_list]
if sub_param.upper().startswith("gl=".upper()):
gl_file_path = sub_param.split("=")[1]
# Parses the gl if supplied
if gl_file_path == None:
gl_dict = None
else:
gl_dict = {}
gl_file = open(gl_file_path).readlines()
for line in gl_file:
gl_dict[line.rstrip().upper()] = True
# Parses the pde file:
pde_file = open(pde_file_path).readlines()
pde_dict = {}
header = True
for line in pde_file:
if header:
header = False
else:
gene, log2fold, p, padj = line.rstrip().split("\t")
gene = gene.upper()
sig = False
if is_number(log2fold):
log2fold_valid = True
log2fold = round(float(log2fold), 2)
else:
log2fold_valid = False
if is_number(p):
p_valid = True
p = float(p)
else:
p_valid = False
if is_number(padj):
padj_valid = True
padj = float(padj)
else:
padj_valid = False
if log2fold_valid and p_valid and padj_valid:
valid = True
if padj < p_threshold and abs(log2fold) > fold_threshold:
sig = True
else:
sig = False
else:
valid = False
in_gl = True
if gl_dict != None:
if gene not in gl_dict:
in_gl = False
# Stores the parsed gene
pde_dict[gene] = {
"sig": sig,
"log2fold": log2fold,
"p": p,
"p.adj": padj,
"valid": valid,
"log2fold_valid": log2fold_valid,
"p_valid": p_valid,
"p.adj_valid": padj_valid,
"in_gl": in_gl
}
# sets the order to the default (numerator+denominator) if unsupplied
if order_list == None:
order_list = [denominator_group, numerator_group]
# Stores the parsed parameter:
pde_parameter_dict = {}
pde_parameter_dict["pde_dict"] = pde_dict
pde_parameter_dict["numerator_group"] = numerator_group
pde_parameter_dict["denominator_group"] = denominator_group
pde_parameter_dict["p_threshold"] = p_threshold
pde_parameter_dict["fold_threshold"] = fold_threshold
pde_parameter_dict["order_list"] = order_list
pde_parameter_dict["gl_dict"] = gl_dict
pde_parameter_dict[
"pde_ID"] = numerator_group + " vs " + denominator_group
pde_parameter_dict["pde_file_path"] = pde_file_path
parsed_pde_parameters.append(pde_parameter_dict)
print "parsed the pde parameter: " + pde_parameter
global_variables["pde_parameters"] = parsed_pde_parameters
return global_variables
def pde_validation(pde_workflow_parameters, sample_groups):
for pde_parameter in pde_workflow_parameters:
# required inputs
pde_file_path = None
numerator = None
denominator = None
# gets the sub-parameters
sub_params_list = pde_parameter.split(",")
# checks the sub params
for sub_param in sub_params_list:
# Tests if there are two parts to the sub-parameter
if len(sub_param.split("=")) != 2:
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " is not in the correct format."
sys.exit(1)
# Tests the file sub-parameter
if sub_param.upper().startswith("file=".upper()):
pde_file_path = sub_param.split("=")[1]
# Tests if the pde file can be opened:
try:
pde_file = open(pde_file_path).readlines()
except:
print >> sys.stderr, "Error: the PDE file: " + pde_file_path + " cannot be opened."
sys.exit(1)
# Tests if the pde file is in the correct format:
line_counter = 1
for line in pde_file:
line_split = line.rstrip().split("\t")
if len(line_split) != 4:
print >> sys.stderr, "Error: the PDE file: " + pde_file_path + " line " + str(
line_counter) + "does not have 4 columns."
sys.exit(1)
if line_counter == 1:
if line_split[0].upper() != "ID":
print >> sys.stderr, "Error: the PDE file: " + pde_file_path + " does not have \"ID\" as the first column in the header."
sys.exit(1)
if line_split[1].upper() != "LOG2FOLD":
print >> sys.stderr, "Error: the PDE file: " + pde_file_path + " does not have \"LOG2FOLD\" as the second column in the header."
sys.exit(1)
if line_split[2].upper() != "P":
print >> sys.stderr, "Error: the PDE file: " + pde_file_path + " does not have \"P\" as the third column in the header."
sys.exit(1)
if line_split[3].upper() != "P.ADJ":
print >> sys.stderr, "Error: the PDE file: " + pde_file_path + " does not have \"P.ADJ\" as the fourth column in the header."
sys.exit(1)
line_counter += 1
# Tests the numerator sub-parameter
if sub_param.upper().startswith("numerator=".upper()):
numerator = sub_param.split("=")[1]
if not is_sample_group(numerator.upper(), sample_groups):
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " \"numerator=\" group is not a valid sample group"
sys.exit(1)
# Tests the numerator sub-parameter
if sub_param.upper().startswith("denominator=".upper()):
denominator = sub_param.split("=")[1]
if not is_sample_group(denominator.upper(), sample_groups):
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " \"denominator=\" group is not a valid sample group"
sys.exit(1)
# Tests the p.adj sub-parameter
if sub_param.upper().startswith("p.adj=".upper()):
padj = sub_param.split("=")[1]
if not is_number(padj):
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " is not in the correct format."
sys.exit(1)
# Tests the log2fold sub-parameter
if sub_param.upper().startswith("p.adj=".upper()):
log2fold = sub_param.split("=")[1]
if not is_number(log2fold):
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " is not in the correct format."
sys.exit(1)
# Tests the order sub-parameter
if sub_param.upper().startswith("order=".upper()):
order_sample_groups = sub_param.split("=")[1].split("+")
if len(order_sample_groups) < 2:
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " does not have at least 2 sample groups in \" order=\""
sys.exit(1)
for sample_group in order_sample_groups:
if not is_sample_group(sample_group.upper(),
sample_groups):
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " has a sample group in \"order=\" that is not in the sample sheet"
sys.exit(1)
# Tests the gene list sub-parameter
if sub_param.upper().startswith("gl=".upper()):
gl_file_path = sub_param.split("=")[1]
try:
gl_file = open(gl_file_path).readlines()
except:
print >> sys.stderr, "Error: the GL file: " + gl_file_path + " cannot be opened."
sys.exit(1)
# tests if the required inputs have been supplied
if pde_file_path == None or numerator == None or denominator == None:
print >> sys.stderr, "Error: the PDE parameter: " + pde_parameter + " is not in the correct format."
sys.exit(1)
print "validated the pde parameter: " + pde_parameter
def mde_validation(mde_workflow_parameters, sample_groups, de_parameters):
# gets the names of the des
de_keys = {}
for de_parameter in de_parameters:
de_keys[de_parameter["de_ID"]] = True
mde_names = {}
for mde_parameter in mde_workflow_parameters:
# required inputs
mde_name = None
# gets the sub-parameters
sub_params_list = mde_parameter.split(",")
#number of des
de_count = 0
# checks the sub params
for sub_param in sub_params_list:
# Tests the name sub-parameter
if sub_param.upper().startswith("name=".upper()):
if len(sub_param.split("=")) != 2:
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format."
sys.exit(1)
mde_name = sub_param.split("=")[1]
if mde_name.upper() in mde_names:
print >> sys.stderr, "Error: the Mde name " + mde_name + " is used more than once."
sys.exit(1)
mde_names[mde_name] = True
# Tests the order sub-parameter
if sub_param.upper().startswith("order=".upper()):
if len(sub_param.split("=")) != 2:
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (order=)."
sys.exit(1)
order = sub_param.split("=")[1].split("+")
if len(order) < 2:
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (> 2 sample groups in order=)"
sys.exit(1)
for sample_group in order:
if not is_sample_group(sample_group.upper(),
sample_groups):
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (order sample group missing from sample sheet"
sys.exit(1)
# Tests the de sub-parameters
if sub_param.upper().startswith("numerator=".upper()):
if len(sub_param.split("*")) != 2:
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (numerator=)."
sys.exit(1)
numerator_string, denominator_string = sub_param.split("*")
if len(numerator_string.split("=")) != 2:
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (numerator=x*deonminator=y)."
sys.exit(1)
if not denominator_string.upper().startswith(
"denominator=".upper()):
print >> sys.stderr, "Error: the Mde parameter " + mde_parameter + " is not in the correct format (denominator=)."
sys.exit(1)
if len(denominator_string.split("=")) != 2:
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (denominator=)."
sys.exit(1)
numerator = numerator_string.split("=")[1]
denominator = denominator_string.split("=")[1]
if not is_sample_group(numerator.upper(), sample_groups):
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (numerator sample group missing from sample sheet)."
sys.exit(1)
if not is_sample_group(denominator.upper(), sample_groups):
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (denominator sample group missing from sample sheet)."
sys.exit(1)
de_ID = numerator.upper() + " vs " + denominator.upper()
if de_ID not in de_keys:
print >> sys.stderr, "Error: the Mde parameter " + mde_parameter + " is not in the correct format (no de parameter of same name): " + de_ID
sys.exit(1)
de_count += 1
# Tests the correlation cut-off sub-parameter
if sub_param.upper().startswith("scc=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the Mde parameter " + mde_parameter + " is not in the correct format (scc is not a number)"
sys.exit(1)
# tests if the required inputs have been supplied
if de_count < 2:
print >> sys.stderr, "Error: the Mde parameter " + mde_parameter + " has fewer than 2 des."
sys.exit(1)
if mde_name == None:
print >> sys.stderr, "Error: the Mde parameter: " + mde_parameter + " is not in the correct format (missing name=)."
sys.exit(1)
print "validated the mde parameter: " + mde_parameter
def background_validation(bg_parameter, global_variables):
# required inputs
background_file_path = None
# gets the sub-parameters
sub_params_list = bg_parameter.split(",")
# checks the sub params
for sub_param in sub_params_list:
# Tests if there are two parts to the sub-parameter
if len(sub_param.split("=")) != 2:
print >> sys.stderr, "Error: the background parameter is not in a valid format."
sys.exit(1)
# Tests the file sub-parameter
if sub_param.upper().startswith("file=".upper()):
background_file_path = sub_param.split("=")[1]
# Tests if the background file can be opened:
try:
background_file = open(background_file_path).readlines()
except:
print >> sys.stderr, "Error: the background file: \"" + str(
background_file_path) + "\" cannot be opened."
sys.exit(1)
line_counter = 1
gene_IDs_dict = {}
for line in background_file:
line_split = line.rstrip().split("\t")
# Validates the header line
if line_counter == 1:
accepted_col_headers = {
"ID": True,
"SYMBOL": True,
"BIOTYPE": True,
"CHROMOSOME": True,
"START": True,
"STOP": True
}
header_dict = {}
for index in range(0, len(line_split)):
header_dict[line_split[index].upper()] = index
if line_split[index].upper(
) not in accepted_col_headers:
print >> sys.stderr, "Error: the background file column header: " + line_split[
index].upper(
) + " is not an accepted column header, e.g. " + "\t\t".join(
accepted_col_headers.keys())
sys.exit(1)
if "ID" not in header_dict:
print >> sys.stderr, "Error: there must be a column called \"ID\" in the background file."
sys.exit(1)
#Sets up the types of background information in the global variables
if "SYMBOL" in header_dict:
global_variables["GENE_SYMBOL_FLAG"] = True
if "BIOTYPE" in header_dict:
global_variables["GENE_BIOTYPE_FLAG"] = True
if "CHROMOSOME" in header_dict:
global_variables["GENE_CHROMOSOME_FLAG"] = True
if "START" in header_dict:
global_variables["GENE_START_FLAG"] = True
if "STOP" in header_dict:
global_variables["GENE_STOP_FLAG"] = True
if global_variables[
"GENE_CHROMOSOME_FLAG"] and global_variables[
"GENE_START_FLAG"] and global_variables[
"GENE_STOP_FLAG"]:
global_variables["GENE_COORDINATES_FLAG"] = True
# Validates the genes
else:
if line_split[header_dict["ID"]] in gene_IDs_dict:
print >> sys.stderr, "Error: line " + str(
line_counter
) + " of the background file has a duplicate gene ID. Gene IDs MUST be unique."
sys.exit(1)
gene_IDs_dict[line_split[header_dict["ID"]]] = True
if len(line_split) != len(header_dict):
print >> sys.stderr, "Error: line " + str(
line_counter
) + " of the background file has more columns than the header line."
sys.exit(1)
if global_variables["GENE_START_FLAG"]:
if not is_number(line_split[header_dict["START"]]):
print >> sys.stderr, "Error: line " + str(
line_counter
) + " of the background file has a start coordinate that is not a number."
sys.exit(1)
if global_variables["GENE_STOP_FLAG"]:
if not is_number(line_split[header_dict["STOP"]]):
print >> sys.stderr, "Error: line " + str(
line_counter
) + " of the background file has a stop coordinate that is not a number."
sys.exit(1)
line_counter += 1
# tests if the required inputs have been supplied
if background_file_path == None:
print >> sys.stderr, "Error: the background parameter is not in a valid format."
sys.exit(1)
print "validated the background parameter"
return global_variables
def normexp_validation(norm_exp_parameter, sample_list):
# required inputs
norm_exp_file_path = None
# gets the sub-parameters
sub_params_list = norm_exp_parameter.split(",")
# checks the sub params
for sub_param in sub_params_list:
# Tests if there are two parts to the sub-parameter
if len(sub_param.split("=")) != 2:
print >> sys.stderr, "Error: the normexp parameter is not in a valid format."
sys.exit(1)
# Tests if the expression threshold is in the correct format
if sub_param.upper().startswith("expressed=".upper()):
if not is_number(sub_param.split("=")[1]):
print >> sys.stderr, "Error: the normexp parameter is not in a valid format."
sys.exit(1)
# Tests the file sub-parameter
if sub_param.upper().startswith("file=".upper()):
norm_exp_file_path = sub_param.split("=")[1]
# Tests if the normexp file can be opened
try:
norm_exp_file = open(norm_exp_file_path).readlines()
except:
print >> sys.stderr, "Error: the normexp file: \"" + str(
norm_exp_file_path) + "\" cannot be opened."
sys.exit(1)
# checks the normexp file contents
line_counter = 1
for line in norm_exp_file:
line_split = line.rstrip().split("\t")
# Validates the header line (samples etc)
if line_counter == 1:
if line_split[0].upper() != "ID":
print >> sys.stderr, "Error: the first column in normexp file is not called \"ID\"."
sys.exit(1)
samples = line_split[1:]
# Checks the diffexp and ss have the same number of samples:
if len(samples) > len(sample_list):
print >> sys.stderr, "Error: there are more samples in the normexp file than in the sample sheet."
sys.exit(1)
if len(samples) < len(sample_list):
print >> sys.stderr, "Error: there are fewer samples in the normexp file than in the sample sheet."
sys.exit(1)
# Checks the samples in the normexp are also in the ss
for sample in samples:
if not is_sample(sample.upper(), sample_list):
print >> sys.stderr, "Error: in the normexp file the sample " + sample.upper(
) + " is not in the sample sheet."
sys.exit(1)
else:
cells = line_split[1:]
for cell in cells:
if not is_number(cell):
print >> sys.stderr, "Error: the normexp file has a cell that is not a number at line " + str(
line_counter) + "."
sys.exit(1)
line_counter += 1
# tests if the required inputs have been supplied
if norm_exp_file_path == None:
print >> sys.stderr, "Error: the normexp parameter is not in a valid format."
sys.exit(1)
print "validated the normexp parameter"
