def getAnnotations(Species,array_type,reannotate_exon_seq,force):
"""Annotate Affymetrix exon array data using files Ensembl data (sync'ed to genome release)."""
global species; species = Species; global test; global test_cluster
test = 'no'; test_cluster = ['TC0701360']; data_type = 'mRNA'
global ensembl_exon_db; global ensembl_exon_db; global exon_clusters; global exon_region_db
ensembl_exon_db,ensembl_annot_db,exon_clusters,intron_clusters,exon_region_db,intron_retention_db,ucsc_splicing_annot_db,ens_transcript_db = EnsemblImport.getEnsemblAssociations(species,data_type,test)
ensembl_probeset_db = importCriticalExonLocations(species,array_type,ensembl_exon_db,force) ###Get Pre-computed genomic locations for critical exons
ensembl_probeset_db = ExonArrayEnsemblRules.annotateExons(ensembl_probeset_db,exon_clusters,ensembl_exon_db,exon_region_db,intron_retention_db,intron_clusters,ucsc_splicing_annot_db); constitutive_gene_db={}
ExonArrayEnsemblRules.exportEnsemblLinkedProbesets(array_type,ensembl_probeset_db,species)
print "\nCritical exon data exported coordinates, exon associations and splicing annotations exported..."
### Change filenames to reflect junction array type
export_filename = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_Ensembl_probesets.txt'; ef=filepath(export_filename)
export_replacement = string.replace(export_filename,'_probe','_'+array_type+'_probe')
er=filepath(export_replacement); shutil.copyfile(ef,er); os.remove(ef) ### Copy file to a new name
### Export full exon seqeunce for probesets/critical exons to replace the original incomplete sequence (used for miRNA analyses)
if reannotate_exon_seq == 'yes':
JunctionArray.reAnnotateCriticalExonSequences(species,array_type)
def buildExonArrayExonAnnotations(species, array_type, force):
### Get UCSC associations (download databases if necessary)
mRNA_Type = 'mrna'; run_from_scratch = 'yes'
export_all_associations = 'no' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species,mRNA_Type,export_all_associations,run_from_scratch,force)
import ExonArrayEnsemblRules; reload(ExonArrayEnsemblRules)
process_from_scratch='yes'
constitutive_source='default'
### Build the databases and return the variables (not used here)
source_biotype = 'mRNA'
if array_type == 'gene': source_biotype = 'gene'
probeset_db,annotate_db,constitutive_gene_db,splicing_analysis_db = ExonArrayEnsemblRules.getAnnotations(process_from_scratch,constitutive_source,source_biotype,species)
def buildExonArrayExonAnnotations(species, array_type, force):
### Get UCSC associations (download databases if necessary)
mRNA_Type = 'mrna'
run_from_scratch = 'yes'
export_all_associations = 'no' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species, mRNA_Type, export_all_associations,
run_from_scratch, force)
import ExonArrayEnsemblRules
reload(ExonArrayEnsemblRules)
process_from_scratch = 'yes'
constitutive_source = 'default'
### Build the databases and return the variables (not used here)
source_biotype = 'mRNA'
if array_type == 'gene': source_biotype = 'gene'
probeset_db, annotate_db, constitutive_gene_db, splicing_analysis_db = ExonArrayEnsemblRules.getAnnotations(
process_from_scratch, constitutive_source, source_biotype, species)
def grabExonIntronPromoterSequences(species,array_type,data_type,output_types):
### output_types could be adjacent intron sequences, adjacent exon sequences, targets exon sequence or promoter
sequence_input_dir_list=[]
if data_type == 'probeset': sequence_input_dir = '/AltResults/AlternativeOutput/'+array_type+'/sequence_input'
if data_type == 'gene': sequence_input_dir = '/ExpressionOutput/'+array_type+'/sequence_input'
dir_list = read_directory(sequence_input_dir)
for input_file in dir_list:
filedir = sequence_input_dir[1:]+'/'+input_file
filter_db = inputResultFiles(filedir,data_type)
export_exon_filename = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_Ensembl_probesets.txt'
ensembl_probeset_db = ExonArrayEnsemblRules.reimportEnsemblProbesetsForSeqExtraction(export_exon_filename,data_type,filter_db)
"""for gene in ensembl_probeset_db:
if gene == 'ENSG00000139737':
for x in ensembl_probeset_db[gene]:
exon_id,((probe_start,probe_stop,probeset_id,exon_class,transcript_clust),ed) = x
print gene, ed.ExonID()
kill"""
analysis_type = 'get_sequence'
dir = 'AltDatabase/ensembl/'+species+'/'; gene_seq_filename = dir+species+'_gene-seq-2000_flank'
ensembl_probeset_db = EnsemblImport.import_sequence_data(gene_seq_filename,ensembl_probeset_db,species,analysis_type)
"""
critical_exon_file = 'AltDatabase/'+species+'/'+ array_type + '/' + array_type+'_critical-exon-seq.txt'
if output_types == 'all' and data_type == 'probeset':
output_types = ['alt-promoter','promoter','exon','adjacent-exons','adjacent-introns']
else: output_types = [output_types]
for output_type in output_types:
sequence_input_dir = string.replace(sequence_input_dir,'_input','_output')
filename = sequence_input_dir[1:]+'/ExportedSequence-'+data_type+'-'+output_type+'.txt'
exportExonIntronPromoterSequences(filename, ensembl_probeset_db,data_type,output_type)
"""
if output_types == 'all' and data_type == 'probeset':
output_types = ['alt-promoter','promoter','exon','adjacent-exons','adjacent-introns']
else: output_types = [output_types]
for output_type in output_types:
sequence_input_dir2 = string.replace(sequence_input_dir,'_input','_output')
filename = sequence_input_dir2[1:]+'/'+input_file[:-4]+'-'+data_type+'-'+output_type+'.txt'
exportExonIntronPromoterSequences(filename, ensembl_probeset_db,data_type,output_type)
def displayExpressionGraph(species,
Platform,
exp_file,
gene,
transpose,
display=True,
showIntrons=False,
analysisType='plot'):
### Get gene annotations (users can provide an Ensembl or symbol)
print 'Importing exon-level expression data for visualization (be patient)...'
import ExonAnalyze_module
global platform
platform = Platform
if platform != 'AltMouse':
gene_annotation_file = "AltDatabase/ensembl/" + species + "/" + species + "_Ensembl-annotations.txt"
else:
gene_annotation_file = "AltDatabase/" + species + "/" + platform + "/" + platform + "_gene_annotations.txt"
genes = []
gene = string.replace(gene, '|', ',')
gene = string.replace(gene, ' ', ',')
if ',' in gene:
genes += string.split(gene, ',')
else:
genes.append(gene)
gene_db = {}
for gene in genes:
try:
if 'ENS' in gene:
try:
annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(
gene_annotation_file, platform,
keyBySymbol=False) ### Make an SQLite call
gene_symbol = annotate_db[gene].Symbol()
else:
try:
annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(
gene_annotation_file, platform, keyBySymbol=True)
gene_symbol = gene
gene = annotate_db[gene].GeneID()
gene_db[gene] = gene_symbol
except Exception:
print gene, 'not in database'
if len(gene_db) == 0:
force_no_gene_found_error
if 'AltResults' in exp_file:
root_dir = string.split(exp_file, 'AltResults')[0] + 'ExonPlots/'
else:
root_dir = string.split(exp_file, 'ExpressionInput')[0] + 'ExonPlots/'
import ExonAnalyze_module
if platform == 'RNASeq': datatype = 'exons'
else: datatype = 'probesets'
export_exon_filename = 'AltDatabase/' + species + '/' + platform + '/' + species + '_Ensembl_' + datatype + '.txt'
if verifyFileLength(export_exon_filename) == 0:
rootdir = string.replace(root_dir, 'ExonPlots/', '')
export_exon_filename = rootdir + '/' + export_exon_filename
import ExonArrayEnsemblRules
ensembl_exon_db = ExonArrayEnsemblRules.reimportEnsemblProbesetsForSeqExtraction(
export_exon_filename, 'gene-probesets',
gene_db) ### Make an SQLite call
filter_db = {}
for gene in ensembl_exon_db:
ensembl_exon_db[gene].sort()
for (index, ed, id) in ensembl_exon_db[gene]:
filter_db[id] = []
try:
os.mkdir(root_dir)
except Exception:
None ### dir exists
print 'Image results being saved to the folder "ExonPlots" in the AltAnalyze results directory.'
importTableEntries(exp_file,
filter_db,
ensembl_exon_db,
gene_db,
root_dir,
transpose,
display,
showIntrons,
analysisType=analysisType) ### Make an SQLite call
def displayExpressionGraph(species,Platform,exp_file,gene,transpose,display=True,showIntrons=False,analysisType='plot'):
### Get gene annotations (users can provide an Ensembl or symbol)
print 'Importing exon-level expression data for visualization (be patient)...'
import ExonAnalyze_module
global platform
platform = Platform
if platform != 'AltMouse': gene_annotation_file = "AltDatabase/ensembl/"+species+"/"+species+"_Ensembl-annotations.txt"
else: gene_annotation_file = "AltDatabase/"+species+"/"+platform+"/"+platform+"_gene_annotations.txt"
genes=[]
gene=string.replace(gene,'|',',')
gene=string.replace(gene,' ',',')
if ',' in gene:
genes += string.split(gene,',')
else: genes.append(gene)
gene_db={}
for gene in genes:
try:
if 'ENS' in gene:
try: annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(gene_annotation_file,platform,keyBySymbol=False) ### Make an SQLite call
gene_symbol = annotate_db[gene].Symbol()
else:
try: annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(gene_annotation_file,platform,keyBySymbol=True)
gene_symbol = gene
gene = annotate_db[gene].GeneID()
gene_db[gene]=gene_symbol
except Exception:
#if len(gene)>0: print gene, 'not in database'
pass
if len(gene_db)==0:
force_no_gene_found_error
if 'AltResults' in exp_file:
root_dir = string.split(exp_file,'AltResults')[0]+'ExonPlots/'
else:
root_dir = string.split(exp_file,'ExpressionInput')[0]+'ExonPlots/'
import ExonAnalyze_module
if platform == 'RNASeq': datatype = 'exons'
else: datatype = 'probesets'
export_exon_filename = 'AltDatabase/'+species+'/'+platform+'/'+species+'_Ensembl_'+datatype+'.txt'
if verifyFileLength(export_exon_filename) == 0:
rootdir = string.replace(root_dir,'ExonPlots/','')
export_exon_filename = rootdir+'/'+export_exon_filename
import ExonArrayEnsemblRules
ensembl_exon_db = ExonArrayEnsemblRules.reimportEnsemblProbesetsForSeqExtraction(export_exon_filename,'gene-probesets',gene_db) ### Make an SQLite call
filter_db = {}
for gene in ensembl_exon_db:
ensembl_exon_db[gene].sort()
for (index,ed,id) in ensembl_exon_db[gene]:
filter_db[id] = []
try: os.mkdir(root_dir)
except Exception: None ### dir exists
print 'Image results being saved to the folder "ExonPlots" in the AltAnalyze results directory.'
importTableEntries(exp_file,filter_db,ensembl_exon_db,gene_db,root_dir,transpose,display,showIntrons,analysisType=analysisType) ### Make an SQLite call
def getJunctionComparisonsFromExport(species,array_type):
type = 'standard'
gene_junction_db = importEnsemblUCSCAltJunctions(species,type)
### Retrieve probesets with exon-junctions associated - these are critical exons
filename = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_Ensembl_'+array_type+'_probesets.txt'
gene_probeset_db = ExonArrayEnsemblRules.reimportEnsemblProbesetsForSeqExtraction(filename,'junctions',{})
left={}; right={}; gene_db={}; gene_exon_db={}; nonjunction_aligning={}
for gene in gene_probeset_db:
for (probe_data,ed) in gene_probeset_db[gene]:
probeset, strand, probeset_start, probeset_stop = probe_data
region_id = string.replace(ed.RegionNumber(),'-','.')
original_region_id = region_id
region_ids = string.split(region_id,'|')
gene_db[probeset[:-2]]=gene
#ed.AssociatedSplicingJunctions()
r_starts=string.split(ed.ExonStart(),'|'); r_stops=string.split(ed.ExonStop(),'|')
for region_id in region_ids:
if '|5' in probeset:
try: left[probeset[:-2]].append(region_id)
except Exception: left[probeset[:-2]]=[region_id]
if strand == '+': ### If the junction probesets DO NOT align to the region coordinates, then the probeset maps to a junction outside the database
if probeset_stop not in r_stops: nonjunction_aligning[probeset[:-2]] = original_region_id+'_'+probeset_stop,'left'
elif probeset_start not in r_starts: nonjunction_aligning[probeset[:-2]] = original_region_id+'_'+probeset_start,'left'
elif '|3' in probeset:
try: right[probeset[:-2]].append(region_id)
except Exception: right[probeset[:-2]]=[region_id]
if strand == '+':
if probeset_start not in r_starts: nonjunction_aligning[probeset[:-2]] = original_region_id+'_'+probeset_start,'right'
elif probeset_stop not in r_stops: nonjunction_aligning[probeset[:-2]] = original_region_id+'_'+probeset_stop,'right'
else:
if '_' in region_id: print killer
try: gene_exon_db[gene,region_id].append(probeset)
except Exception: gene_exon_db[gene,region_id] = [probeset]
print 'len(nonjunction_aligning)',len(nonjunction_aligning)
gene_exon_db = eliminateRedundant(gene_exon_db)
junction_db={} ### Get the exon-region IDs for an exon-junction
for probeset in left:
gene = gene_db[probeset]
if probeset in right:
for region1 in left[probeset]:
for region2 in right[probeset]:
junction = region1+'-'+region2
try: junction_db[gene,junction].append(probeset)
except Exception: junction_db[gene,junction] = [probeset]
probeset_junction_export = 'AltDatabase/' + species + '/'+array_type+'/'+ species + '_junction_comps.txt'
fn=filepath(probeset_junction_export); data = open(fn,'w')
print "Exporting",probeset_junction_export
title = 'gene'+'\t'+'critical_exon'+'\t'+'exclusion_junction_region'+'\t'+'inclusion_junction_region'+'\t'+'exclusion_probeset'+'\t'+'inclusion_probeset'+'\t'+'data_source'+'\n'
data.write(title); temp_list=[]
for (gene,critical_exon,incl_junction,excl_junction) in gene_junction_db:
if (gene,incl_junction) in junction_db:
incl_junction_probesets = junction_db[gene,incl_junction]
if (gene,excl_junction) in junction_db:
excl_junction_probesets = junction_db[gene,excl_junction]
for incl_junction_probeset in incl_junction_probesets:
for excl_junction_probeset in excl_junction_probesets:
try:
for incl_exon_probeset in gene_exon_db[gene,critical_exon]:
if incl_junction_probeset in nonjunction_aligning or excl_junction_probeset in nonjunction_aligning: null=[]
else: ### Ensure the probeset DOES map to the annotated junctions
temp_list.append(string.join([gene,critical_exon,excl_junction,critical_exon,excl_junction_probeset,incl_exon_probeset,'AltAnalyze'],'\t')+'\n')
except Exception: null=[]
if incl_junction_probeset in nonjunction_aligning:
new_region_id, side = nonjunction_aligning[incl_junction_probeset]
incl_junction = renameJunction(incl_junction,side,new_region_id)
if excl_junction_probeset in nonjunction_aligning:
new_region_id, side = nonjunction_aligning[excl_junction_probeset]
excl_junction = renameJunction(excl_junction,side,new_region_id)
if excl_junction_probeset!=incl_junction_probeset:
temp_list.append(string.join([gene,critical_exon,excl_junction,incl_junction,excl_junction_probeset,incl_junction_probeset,'AltAnalyze'],'\t')+'\n')
temp_list = unique.unique(temp_list)
for i in temp_list: data.write(i)
data.close()
print 'Number of compared junctions exported', len(temp_list)
def getAnnotations(fl,Array_type,p_threshold,e_threshold,data_source,manufacturer,constitutive_source,Species,avg_all_for_ss,filter_by_DABG,perform_alt_analysis,expression_data_format):
global species; species = Species; global average_all_probesets; average_all_probesets={}
global avg_all_probes_for_steady_state; avg_all_probes_for_steady_state = avg_all_for_ss; global filter_by_dabg; filter_by_dabg = filter_by_DABG
global dabg_p_threshold; dabg_p_threshold = float(p_threshold); global root_dir; global biotypes; global normalize_feature_exp
global expression_threshold; global exp_data_format; exp_data_format = expression_data_format; global UserOptions; UserOptions = fl
global full_dataset_export_dir; global excludeLowExpressionExons
"""
try: exon_exp_threshold = fl.ExonExpThreshold()
except Exception: exon_exp_threshold = 0
try: exon_rpkm_threshold = fl.ExonRPKMThreshold()
except Exception: exon_rpkm_threshold = 0
try: gene_rpkm_threshold = fl.RPKMThreshold()
except Exception: gene_rpkm_threshold = 0
try: gene_exp_threshold = fl.GeneExpThreshold()
except Exception: gene_exp_threshold = 0
"""
### The input expression data can be log or non-log. If non-log, transform to log in FilterDABG prior to the alternative exon analysis - v.1.16
if expression_data_format == 'log':
try: expression_threshold = math.log(float(e_threshold),2)
except Exception: expression_threshold = 0 ### Applies to RNASeq datasets
else:
expression_threshold = float(e_threshold)
process_from_scratch = 'no' ###internal variables used while testing
global dabg_summary; global expression_summary; dabg_summary={};expression_summary={}
global fulldataset_export_object; global array_type; array_type = Array_type
global exp_analysis_type; exp_analysis_type = 'expression'
global stats_input_dir
expr_input_dir = fl.ExpFile(); stats_input_dir = fl.StatsFile(); root_dir = fl.RootDir()
try: normalize_feature_exp = fl.FeatureNormalization()
except Exception: normalize_feature_exp = 'NA'
try: excludeLowExpressionExons = fl.excludeLowExpressionExons()
except Exception: excludeLowExpressionExons = True
try:
useJunctionsForGeneExpression = fl.useJunctionsForGeneExpression()
if useJunctionsForGeneExpression:
print 'Using known junction only to estimate gene expression!!!'
except Exception: useJunctionsForGeneExpression = False
source_biotype = 'mRNA'
if array_type == 'gene': source_biotype = 'gene'
elif array_type == 'junction': source_biotype = 'junction'
###Get annotations using Affymetrix as a trusted source or via links to Ensembl
if array_type == 'AltMouse':
probeset_db,constitutive_gene_db = ExpressionBuilder.importAltMerge('full'); annotate_db={}
source_biotype = 'AltMouse'
elif manufacturer == 'Affymetrix' or array_type == 'RNASeq':
if array_type == 'RNASeq':
source_biotype = array_type, root_dir
probeset_db,annotate_db,constitutive_gene_db,splicing_analysis_db = ExonArrayEnsemblRules.getAnnotations(process_from_scratch,constitutive_source,source_biotype,species)
### Get all file locations and get array headers
#print len(splicing_analysis_db),"genes included in the splicing annotation database (constitutive only containing)"
stats_file_status = verifyFile(stats_input_dir)
array_linker_db,array_names = importExonProbesetData(expr_input_dir,{},'arraynames')
input_dir_split = string.split(expr_input_dir,'/')
full_dataset_export_dir = root_dir+'AltExpression/FullDatasets/ExonArray/'+species+'/'+string.replace(input_dir_split[-1],'exp.','')
if array_type == 'gene': full_dataset_export_dir = string.replace(full_dataset_export_dir,'ExonArray','GeneArray')
if array_type == 'junction': full_dataset_export_dir = string.replace(full_dataset_export_dir,'ExonArray','JunctionArray')
if array_type == 'AltMouse': full_dataset_export_dir = string.replace(full_dataset_export_dir,'ExonArray','AltMouse')
if array_type == 'RNASeq': full_dataset_export_dir = string.replace(full_dataset_export_dir,'ExonArray','RNASeq')
try: fulldataset_export_object = export.ExportFile(full_dataset_export_dir)
except Exception:
print 'AltAnalyze is having trouble creating the directory:\n',full_dataset_export_dir
print 'Report this issue to the AltAnalyze help desk or create this directory manually (Error Code X1).'; force_exception
### Organize arrays according to groups and export all probeset data and any pairwise comparisons
data_type = 'expression'
if array_type == 'RNASeq':
expr_input_dir = string.replace(expr_input_dir,'exp.','counts.') ### Filter based on the counts file and then replace values with the normalized as the last step
comparison_filename_list,biotypes = exportGroupedComparisonProbesetData(expr_input_dir,probeset_db,data_type,array_names,array_linker_db,perform_alt_analysis)
if useJunctionsForGeneExpression:
if 'junction' in biotypes:
if 'exon' in biotypes: del biotypes['exon']
if filter_by_dabg == 'yes' and stats_file_status == 'found':
data_type = 'dabg'
exportGroupedComparisonProbesetData(stats_input_dir,probeset_db,data_type,array_names,array_linker_db,perform_alt_analysis)
###Filter expression data based on DABG and annotation filtered probesets (will work without DABG filtering as well) - won't work for RNA-Seq (execute function later)
filtered_exon_db = removeNonExpressedProbesets(probeset_db,full_dataset_export_dir)
filterExpressionData(expr_input_dir,filtered_exon_db,constitutive_gene_db,probeset_db,'expression',array_names,perform_alt_analysis)
constitutive_gene_db={}; probeset_gene_db = makeGeneLevelAnnotations(probeset_db)
if array_type == 'RNASeq':
fulldataset_export_object = export.ExportFile(full_dataset_export_dir)
data_type = 'expression' ### Repeat with counts and then with exp. to add gene-level estimates to both
exportGroupedComparisonProbesetData(expr_input_dir,probeset_db,data_type,array_names,array_linker_db,perform_alt_analysis)
fulldataset_export_object = export.ExportFile(full_dataset_export_dir)
expr_input_dir = string.replace(expr_input_dir,'counts.','exp.')
exportGroupedComparisonProbesetData(expr_input_dir,probeset_db,data_type,array_names,array_linker_db,perform_alt_analysis)
try: clearObjectsFromMemory(average_all_probesets); clearObjectsFromMemory(expression_summary); clearObjectsFromMemory(splicing_analysis_db)
except Exception: null=[]
filtered_exon_db=[]; probeset_db={}; average_all_probesets={}; expression_summary={}; splicing_analysis_db={}
#filtered_exp_db,group_count,ranked_array_headers = filterExpressionData(expr_input_dir,filtered_exon_db,constitutive_gene_db,probeset_db)
#filtered_gene_db = permformFtests(filtered_exp_db,group_count,probeset_db)
"""
pre_filtered_db=[]
print 'global vars'
returnLargeGlobalVars()
print 'local vars'
all = [var for var in locals() if (var[:2], var[-2:]) != ("__", "__")]
for var in all:
try:
if len(locals()[var])>500: print var, len(locals()[var])
except Exception: null=[]
"""
return probeset_gene_db, annotate_db, comparison_filename_list
grabExonIntronPromoterSequences(Species,Array_type,Data_type,Output_types)
sys.exit()
#"""
avg_all_for_ss = 'yes'
import_dir = '/AltDatabase/'+Species+ '/exon'
expr_file_dir = 'ExpressionInput\exp.HEK-confluency.plier.txt'
dagb_p = 0.001
f_cutoff = 2.297
exons_to_grab = "core"
x = 'Affymetrix'
y = 'Ensembl'
z = 'default'
data_source = y
constitutive_source = z
filename = expr_file_dir; p = dagb_p
getAnnotations(expr_file_dir,dagb_p,exons_to_grab,data_source,constitutive_source,Species)
global species; species = Species
process_from_scratch = 'no'
###Get annotations using Affymetrix as a trusted source or via links to Ensembl
if data_source == 'Affymetrix':
annotation_dbases = ExonArrayAffyRules.getAnnotations(exons_to_grab,constitutive_source,process_from_scratch)
probe_association_db,constitutive_gene_db,exon_location_db, trans_annotation_db, trans_annot_extended = annotation_dbases
else:
probeset_db,annotate_db,constitutive_gene_db,splicing_analysis_db = ExonArrayEnsemblRules.getAnnotations(process_from_scratch,constitutive_source,species,avg_all_for_ss)
filterExpressionData(filename,filtered_exon_db,constitutive_gene_db,probeset_db,data_type)
#filtered_gene_db = permformFtests(filtered_exp_db,group_count,probeset_db)
