def ForceCriticalError(print_out):
print print_out
if len(
sys.argv[1:]
) < 2: ### Don't create a Tkinter window if command-line options supplied
try:
UI.WarningWindow(print_out, 'Error Encountered!')
root.destroy()
GO_Elite.importGOEliteParameters('yes')
sys.exit()
except Exception:
sys.exit()
sys.exit()
def importDataSimple(filename,input_type,MOD=None,Species=None):
id_db={}
fn = filepath(filename)
x=0
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data,'\t')
if data[0]=='#' and x==0: x=0
elif x==0:
column_headers = t[1:]
if input_type != 'LineageProfiler':
try: column_headers = t[2] ### exclude the ID, system code and p-value column headers
except Exception: column_headers = 'NA'
x=1
else:
if x==1 and input_type != 'LineageProfiler':
### get system conversions
system_code = t[1]
import GO_Elite
import OBO_import
system_codes,source_types,mod_types = GO_Elite.getSourceData()
source_data = system_codes[system_code]
try:
Mod=mod ### global established in upstream functions
speciescode = species_code
except Exception:
Mod=MOD
speciescode = Species
if source_data == Mod:
source_is_mod = True
else:
source_is_mod = False
mod_source = Mod+'-'+source_data+'.txt'
gene_to_source_id = gene_associations.getGeneToUid(speciescode,('hide',mod_source))
source_to_gene = OBO_import.swapKeyValues(gene_to_source_id)
if input_type != 'LineageProfiler':
if source_is_mod == True:
try: id_db[t[0]] = float(t[2])
except Exception: id_db[t[0]] = 'NA'
elif t[0] in source_to_gene:
mod_ids = source_to_gene[t[0]]
for mod_id in mod_ids:
try: value = t[2]
except Exception: value = 'NA'
if value == '+': value = 1
elif value == '-': value = -1
try: id_db[mod_id] = float(value) ### If multiple Ensembl IDs in dataset, only record the last associated fold change
except Exception: id_db[mod_id] = 'NA'
break
else:
id_db[t[0]]= map(float,t[1:]) ### Applies to LineageProfiler
x+=1
#print len(id_db),column_headers
return id_db,column_headers
def importDataSimple(filename, input_type):
id_db = {}
fn = filepath(filename)
x = 0
for line in open(fn, 'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data, '\t')
if data[0] == '#': x = 0
elif x == 0:
column_headers = t[1:]
if input_type != 'LineageProfiler':
column_headers = t[
2] ### exclude the ID, system code and p-value column headers
x = 1
else:
if x == 1 and input_type != 'LineageProfiler':
### get system conversions
system_code = t[1]
import GO_Elite
import OBO_import
system_codes, source_types, mod_types = GO_Elite.getSourceData(
)
source_data = system_codes[system_code]
if source_data == mod:
source_is_mod = True
else:
source_is_mod = False
mod_source = mod + '-' + source_data + '.txt'
gene_to_source_id = gene_associations.getGeneToUid(
species_code, ('hide', mod_source))
source_to_gene = OBO_import.swapKeyValues(
gene_to_source_id)
if input_type != 'LineageProfiler':
if source_is_mod == True:
id_db[t[0]] = float(t[2])
elif t[0] in source_to_gene:
mod_ids = source_to_gene[t[0]]
for mod_id in mod_ids:
id_db[mod_id] = float(
t[2]
) ### If multiple Ensembl IDs in dataset, only record the last associated fold chagne
else:
id_db[t[0]] = map(float, t[1:]) ### Applies to LineageProfiler
x += 1
return id_db, column_headers
def importOntologyAnnotations(species_code, ontology_type):
try:
system_codes, source_types, mod_types = GO_Elite.getSourceData()
verified_nested = OBO_import.verifyNestedFileCreation(
species_code, mod_types, ontology_type)
if verified_nested == 'no': force_error
ontology_annotations = OBO_import.importPreviousOntologyAnnotations(
ontology_type)
except Exception:
try:
### Occurs when the annotation file isn't built yet - if so try to build
OBO_import.buildNestedOntologyAssociations(species_code, mod_types,
ontology_type)
ontology_annotations = OBO_import.importPreviousOntologyAnnotations(
ontology_type)
except Exception:
ontology_annotations = None
return ontology_annotations
def importDataSimple(filename, input_type, MOD=None, Species=None):
id_db = {}
fn = filepath(filename)
x = 0
for line in open(fn, 'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data, '\t')
if data[0] == '#' and x == 0: x = 0
elif x == 0:
column_headers = t[1:]
if input_type != 'LineageProfiler':
try:
column_headers = t[
2] ### exclude the ID, system code and p-value column headers
except Exception:
column_headers = 'NA'
x = 1
else:
if x == 1 and input_type != 'LineageProfiler':
### get system conversions
system_code = t[1]
import GO_Elite
import OBO_import
system_codes, source_types, mod_types = GO_Elite.getSourceData(
)
source_data = system_codes[system_code]
try:
Mod = mod ### global established in upstream functions
speciescode = species_code
except Exception:
Mod = MOD
speciescode = Species
if source_data == Mod:
source_is_mod = True
else:
source_is_mod = False
mod_source = Mod + '-' + source_data + '.txt'
gene_to_source_id = gene_associations.getGeneToUid(
speciescode, ('hide', mod_source))
source_to_gene = OBO_import.swapKeyValues(
gene_to_source_id)
if input_type != 'LineageProfiler':
if source_is_mod == True:
try:
id_db[t[0]] = float(t[2])
except Exception:
id_db[t[0]] = 'NA'
elif t[0] in source_to_gene:
mod_ids = source_to_gene[t[0]]
for mod_id in mod_ids:
try:
value = t[2]
except Exception:
value = 'NA'
if value == '+': value = 1
elif value == '-': value = -1
try:
id_db[mod_id] = float(
value
) ### If multiple Ensembl IDs in dataset, only record the last associated fold change
except Exception:
id_db[mod_id] = 'NA'
break
else:
id_db[t[0]] = map(float, t[1:]) ### Applies to LineageProfiler
x += 1
#print len(id_db),column_headers
return id_db, column_headers