def runProgram(Species,Array_type,mir_source,stringency,Force):
global species; global array_type; global force
process_microRNA_predictions = 'yes'
species = Species; array_type = Array_type; force = Force
import_dir = '/AltDatabase/'+species+'/'+array_type
filedir = import_dir[1:]+'/'
dir_list = read_directory(import_dir) #send a sub_directory to a function to identify all files in a directory
probeset_seq_file=''
for input_file in dir_list: #loop through each file in the directory to results
if 'critical-exon-seq_updated' in input_file: probeset_seq_file = filedir+input_file
elif 'critical-exon-seq' in input_file: probeset_seq_file2 = filedir+input_file
if len(probeset_seq_file)==0: probeset_seq_file=probeset_seq_file2
data_type = 'critical-exons'
try: splice_event_db = getParametersAndExecute(probeset_seq_file,array_type,species,data_type)
except UnboundLocalError:
probeset_seq_file = 'AltDatabase/'+species+'/'+array_type+'/'+array_type+'_critical-exon-seq_updated.txt'
update.downloadCurrentVersion(probeset_seq_file,array_type,'txt')
splice_event_db = getParametersAndExecute(probeset_seq_file,array_type,species,data_type)
if process_microRNA_predictions == 'yes':
print 'stringency:',stringency
try:
ensembl_mirna_db = ExonSeqModule.importmiRNATargetPredictionsAdvanced(species)
ExonSeqModule.alignmiRNAData(array_type,mir_source,species,stringency,ensembl_mirna_db,splice_event_db)
except Exception: pass
def runProgram(Species, Array_type, mir_source, stringency, Force):
global species
global array_type
global force
process_microRNA_predictions = 'yes'
species = Species
array_type = Array_type
force = Force
import_dir = '/AltDatabase/' + species + '/' + array_type
filedir = import_dir[1:] + '/'
dir_list = read_directory(
import_dir
) #send a sub_directory to a function to identify all files in a directory
probeset_seq_file = ''
for input_file in dir_list: #loop through each file in the directory to results
if 'critical-exon-seq_updated' in input_file:
probeset_seq_file = filedir + input_file
elif 'critical-exon-seq' in input_file:
probeset_seq_file2 = filedir + input_file
if len(probeset_seq_file) == 0: probeset_seq_file = probeset_seq_file2
data_type = 'critical-exons'
try:
splice_event_db = getParametersAndExecute(probeset_seq_file,
array_type, species,
data_type)
except UnboundLocalError:
probeset_seq_file = 'AltDatabase/' + species + '/' + array_type + '/' + array_type + '_critical-exon-seq_updated.txt'
update.downloadCurrentVersion(probeset_seq_file, array_type, 'txt')
splice_event_db = getParametersAndExecute(probeset_seq_file,
array_type, species,
data_type)
if process_microRNA_predictions == 'yes':
print 'stringency:', stringency
try:
ensembl_mirna_db = ExonSeqModule.importmiRNATargetPredictionsAdvanced(
species)
ExonSeqModule.alignmiRNAData(array_type, mir_source, species,
stringency, ensembl_mirna_db,
splice_event_db)
except Exception:
pass