def geneCoordinates(species,symbols):
genes=[]
import EnsemblImport
ensembl_annotation_db = EnsemblImport.reimportEnsemblAnnotations(species,symbolKey=True)
for symbol in symbols:
ens_geneid = ensembl_annotation_db[symbol]
genes.append((ens_geneid,symbol))
### Get gene genomic locations
gene_location_db = EnsemblImport.getEnsemblGeneLocations(species,'RNASeq','key_by_array')
search_locations=[]
for (gene,symbol) in genes:
chr,strand,start,end = gene_location_db[gene]
if symbol == 'SRSF10': chr = 'chr1'; strand = '-'; start = '24295573'; end = '24306953'
if len(chr)>6: print symbol, 'bad chromosomal reference:',chr
else:
search_locations.append([chr,strand,start,end,symbol])
def alignProbesetsToTranscripts(species,array_type,Analysis_type,Force, CoordinateBasedMatching = False):
global force; force = Force; global analysis_type; analysis_type = Analysis_type
global coordinateBasedMatching; coordinateBasedMatching = CoordinateBasedMatching
"""Match exon or junction probeset sequences to Ensembl and USCS mRNA transcripts"""
if array_type == 'AltMouse' or array_type == 'junction' or array_type == 'RNASeq':
data_type = 'junctions'; probeset_seq_file=''; biotype = 'gene'
if data_type == 'junctions' and analysis_type == 'reciprocal':
start_time = time.time() ### Indicates whether to store information at the level of genes or probesets
probeset_seq_db,pairwise_probeset_combinations = importJunctionAnnotationDatabaseAndSequence(species,array_type,biotype)
end_time = time.time(); time_diff = int(end_time-start_time)
elif analysis_type == 'single':
start_time = time.time()
probeset_seq_db,pairwise_probeset_combinations = importAllJunctionSequences(species,array_type)
end_time = time.time(); time_diff = int(end_time-start_time)
print "Analyses finished in %d seconds" % time_diff
elif array_type == 'exon':
data_type = 'exon'
probeset_annotations_file = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_Ensembl_probesets.txt'
###Import probe-level associations
exon_db = importSplicingAnnotationDatabase(probeset_annotations_file)
start_time = time.time()
probeset_seq_db = importProbesetSequences(exon_db,species)
end_time = time.time(); time_diff = int(end_time-start_time)
print "Analyses finished in %d seconds" % time_diff
### Match probesets to mRNAs\=
import EnsemblImport
if coordinateBasedMatching == True and array_type == 'RNASeq':
EnsemblImport.exportTranscriptExonIDAssociations(species)
matchTranscriptExonIDsToJunctionIDs(species,array_type,probeset_seq_db) ### no sequences in probeset_seq_db, just junctionIDs
else:
#matchTranscriptExonIDsToJunctionIDs(species,array_type,probeset_seq_db) ### no sequences in probeset_seq_db, just junctionIDs
importEnsemblTranscriptSequence(species,array_type,probeset_seq_db)
try: mRNASeqAlign.importUCSCTranscriptSequences(species,array_type,probeset_seq_db)
except Exception: pass ### If the species not supported by UCSC - the UCSC file is not written, but the other mRNA_alignments files should be available
probeset_seq_db={} ### Re-set db
### Import results if junction array to make comparisons valid for junction-pairs rather than a single probeset
if data_type == 'junctions':
### Re-import matches from above and export matching and non-matching transcripts for each probeset to a new file
import_dir = '/AltDatabase/'+species+'/SequenceData/output'
g = GrabFiles(); g.setdirectory(import_dir)
align_files = g.searchdirectory('mRNA_alignments')
reAnalyzeRNAProbesetMatches(align_files,species,array_type,pairwise_probeset_combinations)
def findSpeciesInUniProtFiles(force):
### Download all UniProt annotation files and grab all species names, TaxIDs and corresponding URLs
import AltAnalyze
###Get species annotations from the GO-Elite config
species_annot_db=AltAnalyze.importGOEliteSpeciesInfo(); tax_db={}
for species_full in species_annot_db:
taxid=species_annot_db[species_full].TaxID()
tax_db[taxid]=species_full
if force == 'yes':
### Should only need to be run if UniProt changes it's species to file associations or new species supported by Ensembl
import export; import update
filesearch = '_sprot_'
all_swissprot = update.getFTPData('ftp.expasy.org','/databases/uniprot/current_release/knowledgebase/taxonomic_divisions',filesearch)
for file in all_swissprot:
gz_filepath, status = update.download(file,'uniprot_temp/','')
if status == 'not-removed':
try: os.remove(gz_filepath) ### Not sure why this works now and not before
except OSError: status = status
species_uniprot_db={}; altanalyze_species_uniprot_db={}
dir=read_directory('/uniprot_temp')
for filename in dir:
fn=filepath('uniprot_temp/'+filename)
for line in open(fn,'r').xreadlines():
data = cleanUpLine(line)
if data[0:2] == 'OX':
taxid = string.split(data,'=')[1][:-1]
if taxid in tax_db:
species_full = tax_db[taxid]
elif data[0:2] == 'OS':
species = data[5:]
species = string.split(species,' ')[:2]
species_full = string.join(species,' ')
elif data[0] == '/':
url = 'ftp.expasy.org/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/'+filename
ss = string.split(species_full,' ')
if len(ss)==2: ### Species name is in the format H**o sapiens - and '(' not in species_full and ')' not in species_full and '/' not in species_full
try: species_uniprot_db[species_full].append((taxid,'ftp://'+url+'.gz'))
except KeyError: species_uniprot_db[species_full] = [(taxid,'ftp://'+url+'.gz')]
taxid = ''; species_full = ''
import EnsemblImport
species_uniprot_db = EnsemblImport.eliminate_redundant_dict_values(species_uniprot_db)
### Export all species to UniProt file relationships so this function needs to only be run once
import export
up = export.ExportFile('Config/uniprot-species-file.txt')
for species_full in species_uniprot_db:
values = species_uniprot_db[species_full]
if len(values)>1:
found = 'no'
for (taxid,url) in values:
if taxid in tax_db:
if species_full == tax_db[taxid]: found='yes'; print 'ambiguity resolved:',species_full; break
if found == 'yes': break
else: (taxid,url) = values[0]
up.write(string.join([species_full,taxid,url],'\t')+'\n')
up.close()
def findSpeciesInUniProtFiles(force):
### Download all UniProt annotation files and grab all species names, TaxIDs and corresponding URLs
import AltAnalyze
###Get species annotations from the GO-Elite config
species_annot_db=AltAnalyze.importGOEliteSpeciesInfo(); tax_db={}
for species_full in species_annot_db:
taxid=species_annot_db[species_full].TaxID()
tax_db[taxid]=species_full
if force == 'yes':
### Should only need to be run if UniProt changes it's species to file associations or new species supported by Ensembl
import export; import update
filesearch = '_sprot_'
all_swissprot = update.getFTPData('ftp.expasy.org','/databases/uniprot/current_release/knowledgebase/taxonomic_divisions',filesearch)
for file in all_swissprot:
gz_filepath, status = update.download(file,'uniprot_temp/','')
if status == 'not-removed':
try: os.remove(gz_filepath) ### Not sure why this works now and not before
except OSError: status = status
species_uniprot_db={}; altanalyze_species_uniprot_db={}
dir=read_directory('/uniprot_temp')
for filename in dir:
fn=filepath('uniprot_temp/'+filename)
for line in open(fn,'r').xreadlines():
data = cleanUpLine(line)
if data[0:2] == 'OX':
taxid = string.split(data,'=')[1][:-1]
if taxid in tax_db:
species_full = tax_db[taxid]
elif data[0:2] == 'OS':
species = data[5:]
species = string.split(species,' ')[:2]
species_full = string.join(species,' ')
elif data[0] == '/':
url = 'ftp.expasy.org/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/'+filename
ss = string.split(species_full,' ')
if len(ss)==2: ### Species name is in the format H**o sapiens - and '(' not in species_full and ')' not in species_full and '/' not in species_full
try: species_uniprot_db[species_full].append((taxid,'ftp://'+url+'.gz'))
except KeyError: species_uniprot_db[species_full] = [(taxid,'ftp://'+url+'.gz')]
taxid = ''; species_full = ''
import EnsemblImport
species_uniprot_db = EnsemblImport.eliminate_redundant_dict_values(species_uniprot_db)
### Export all species to UniProt file relationships so this function needs to only be run once
import export
up = export.ExportFile('Config/uniprot-species-file.txt')
for species_full in species_uniprot_db:
values = species_uniprot_db[species_full]
if len(values)>1:
found = 'no'
for (taxid,url) in values:
if taxid in tax_db:
if species_full == tax_db[taxid]: found='yes'; print 'ambiguity resolved:',species_full; break
if found == 'yes': break
else: (taxid,url) = values[0]
up.write(string.join([species_full,taxid,url],'\t')+'\n')
up.close()
def geneCoordinates(species,symbols):
genes=[]
import EnsemblImport
ensembl_annotation_db = EnsemblImport.reimportEnsemblAnnotations(species,symbolKey=True)
for symbol in symbols:
if symbol in ensembl_annotation_db:
ens_geneid = ensembl_annotation_db[symbol]
genes.append((ens_geneid,symbol))
else:
print symbol, 'not found'
### Get gene genomic locations
gene_location_db = EnsemblImport.getEnsemblGeneLocations(species,'RNASeq','key_by_array')
search_locations=[]
for (gene,symbol) in genes:
chr,strand,start,end = gene_location_db[gene]
#if symbol == 'SRSF10': chr = 'chr1'; strand = '-'; start = '24295573'; end = '24306953'
if len(chr)>6: print symbol, 'bad chromosomal reference:',chr
else:
search_locations.append([chr,strand,start,end,symbol])
def exportChromosomeStrandCoordinates(species):
import EnsemblImport
gene_location_db = EnsemblImport.getEnsemblGeneLocations(
species, 'RNASeq', 'key_by_array')
import ExpressionBuilder
gene_biotype_db = ExpressionBuilder.importTranscriptBiotypeAnnotations(
species)
export_path = 'GenMAPPDBs/' + species + '/chr_gene_locations.txt'
export_data = export.ExportFile(export_path)
import ExonAnalyze_module
gene_annotation_file = "AltDatabase/ensembl/" + species + "/" + species + "_Ensembl-annotations.txt"
annotate_db = ExonAnalyze_module.import_annotations(
gene_annotation_file, 'RNASeq')
print 'Annotations for', len(gene_location_db), 'genes imported'
sorted_list = []
protein_coding = 0
for gene in gene_location_db:
chr, strand, start, end = gene_location_db[gene]
if gene in gene_biotype_db:
biotype = gene_biotype_db[gene][-1]
if biotype == 'protein_coding': protein_coding += 1
else: biotype = 'NA'
if len(chr) < 7:
sorted_list.append(
[chr, strand, int(start),
int(end), gene, biotype])
#else: print chr;sys.exit()
print len(sorted_list), 'genes for typical chromosomes present'
print protein_coding, 'protein coding genes present'
sorted_list.sort()
for values in sorted_list:
chr, strand, start, end, gene, biotype = values
try:
symbol = annotate_db[gene].Symbol()
except Exception:
symbol = ''
values = [gene, symbol, chr, strand, str(start), str(end), biotype]
export_data.write(string.join(values, '\t') + '\n')
export_data.close()
print species, 'chromosome locations exported to:\n', export_path
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 exportChromosomeStrandCoordinates(species):
import EnsemblImport
gene_location_db = EnsemblImport.getEnsemblGeneLocations(species,'RNASeq','key_by_array')
import ExpressionBuilder
gene_biotype_db = ExpressionBuilder.importTranscriptBiotypeAnnotations(species)
export_path = 'GenMAPPDBs/'+species+'/chr_gene_locations.txt'
export_data = export.ExportFile(export_path)
import ExonAnalyze_module
gene_annotation_file = "AltDatabase/ensembl/"+species+"/"+species+"_Ensembl-annotations.txt"
annotate_db = ExonAnalyze_module.import_annotations(gene_annotation_file,'RNASeq')
print 'Annotations for',len(gene_location_db),'genes imported'
sorted_list=[]; protein_coding=0
for gene in gene_location_db:
chr,strand,start,end = gene_location_db[gene]
if gene in gene_biotype_db:
biotype = gene_biotype_db[gene][-1]
if biotype == 'protein_coding': protein_coding+=1
else: biotype = 'NA'
if len(chr)<7:
sorted_list.append([chr,strand,int(start),int(end),gene,biotype])
#else: print chr;sys.exit()
print len(sorted_list),'genes for typical chromosomes present'
print protein_coding, 'protein coding genes present'
sorted_list.sort()
for values in sorted_list:
chr,strand,start,end,gene,biotype=values
try: symbol = annotate_db[gene].Symbol()
except Exception: symbol = ''
values = [gene,symbol,chr,strand,str(start),str(end),biotype]
export_data.write(string.join(values,'\t')+'\n')
export_data.close()
print species, 'chromosome locations exported to:\n',export_path
def reformatPolyAdenylationCoordinates(species,force):
""" PolyA annotations are currently only available from UCSC for human, but flat file
annotations from 2003-2006 are available for multiple species. Convert these to BED format"""
version={}
version['Rn'] = '2003(rn3)'
version['Dr'] = '2003(zv4)'
version['Gg'] = '2004(galGal2)'
version['Hs'] = '2006(hg8)'
version['Mm'] = '2004(mm5)'
print 'Exporting polyADB_2 coordinates as BED for',species
### Obtain the necessary database files
url = 'http://altanalyze.org/archiveDBs/all/polyAsite.txt'
output_dir = 'AltDatabase/ucsc/'+species + '/'
if force == 'yes':
filename, status = update.download(url,output_dir,'')
else: filename = output_dir+'polyAsite.txt'
### Import the refseq to Ensembl information
import gene_associations; import OBO_import; import EnsemblImport; import export
try:
ens_unigene = gene_associations.getGeneToUid(species,'Ensembl-UniGene')
print len(ens_unigene),'Ensembl-UniGene entries imported'
external_ensembl = OBO_import.swapKeyValues(ens_unigene); use_entrez='no'
except Exception:
ens_entrez = gene_associations.getGeneToUid(species,'Ensembl-EntrezGene')
print len(ens_entrez),'Ensembl-EntrezGene entries imported'
external_ensembl = OBO_import.swapKeyValues(ens_entrez); use_entrez='yes'
gene_location_db = EnsemblImport.getEnsemblGeneLocations(species,'RNASeq','key_by_array')
export_bedfile = output_dir+species+'_polyADB_2_predictions.bed'
print 'exporting',export_bedfile
export_data = export.ExportFile(export_bedfile)
header = '#'+species+'\t'+'polyADB_2'+'\t'+version[species]+'\n'
export_data.write(header)
fn=filepath(filename); x=0; not_found={}
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line)
if x==0: x=1
else:
siteid,llid,chr,sitenum,position,supporting_EST,cleavage = string.split(data,'\t')
if chr == 'chrM': chr = 'chrMT' ### MT is the Ensembl convention whereas M is the Affymetrix and UCSC convention
if chr == 'M': chr = 'MT' ### MT is the Ensembl convention whereas M is the Affymetrix and UCSC convention
if species in siteid:
if 'NA' not in chr: chr = 'chr'+chr
strand = '+'; geneid = siteid
pos_start = str(int(position)-1); pos_end = position
if use_entrez=='no':
external_geneid = string.join(string.split(siteid,'.')[:2],'.')
else: external_geneid=llid
if external_geneid in external_ensembl:
ens_geneid = external_ensembl[external_geneid][0]
geneid += '-'+ens_geneid
chr,strand,start,end = gene_location_db[ens_geneid]
else:
not_found[external_geneid]=[]
bed_format = string.join([chr,pos_start,pos_end,geneid,'0','-'],'\t')+'\n' ### We don't know the strand, so write out both strands
export_data.write(bed_format)
bed_format = string.join([chr,pos_start,pos_end,geneid,'0',strand],'\t')+'\n'
export_data.write(bed_format)
export_data.close()
def alignProbesetsToTranscripts(species,
array_type,
Analysis_type,
Force,
CoordinateBasedMatching=False):
global force
force = Force
global analysis_type
analysis_type = Analysis_type
global coordinateBasedMatching
coordinateBasedMatching = CoordinateBasedMatching
"""Match exon or junction probeset sequences to Ensembl and USCS mRNA transcripts"""
if array_type == 'AltMouse' or array_type == 'junction' or array_type == 'RNASeq':
data_type = 'junctions'
probeset_seq_file = ''
biotype = 'gene'
if data_type == 'junctions' and analysis_type == 'reciprocal':
start_time = time.time(
) ### Indicates whether to store information at the level of genes or probesets
probeset_seq_db, pairwise_probeset_combinations = importJunctionAnnotationDatabaseAndSequence(
species, array_type, biotype)
end_time = time.time()
time_diff = int(end_time - start_time)
elif analysis_type == 'single':
start_time = time.time()
probeset_seq_db, pairwise_probeset_combinations = importAllJunctionSequences(
species, array_type)
end_time = time.time()
time_diff = int(end_time - start_time)
print "Analyses finished in %d seconds" % time_diff
elif array_type == 'exon':
data_type = 'exon'
probeset_annotations_file = 'AltDatabase/' + species + '/' + array_type + '/' + species + '_Ensembl_probesets.txt'
###Import probe-level associations
exon_db = importSplicingAnnotationDatabase(probeset_annotations_file)
start_time = time.time()
probeset_seq_db = importProbesetSequences(exon_db, species)
end_time = time.time()
time_diff = int(end_time - start_time)
print "Analyses finished in %d seconds" % time_diff
### Match probesets to mRNAs\=
import EnsemblImport
if coordinateBasedMatching == True and array_type == 'RNASeq':
EnsemblImport.exportTranscriptExonIDAssociations(species)
matchTranscriptExonIDsToJunctionIDs(
species, array_type, probeset_seq_db
) ### no sequences in probeset_seq_db, just junctionIDs
else:
#matchTranscriptExonIDsToJunctionIDs(species,array_type,probeset_seq_db) ### no sequences in probeset_seq_db, just junctionIDs
importEnsemblTranscriptSequence(species, array_type, probeset_seq_db)
try:
mRNASeqAlign.importUCSCTranscriptSequences(species, array_type,
probeset_seq_db)
except Exception:
pass ### If the species not supported by UCSC - the UCSC file is not written, but the other mRNA_alignments files should be available
probeset_seq_db = {} ### Re-set db
### Import results if junction array to make comparisons valid for junction-pairs rather than a single probeset
if data_type == 'junctions':
### Re-import matches from above and export matching and non-matching transcripts for each probeset to a new file
import_dir = '/AltDatabase/' + species + '/SequenceData/output'
g = GrabFiles()
g.setdirectory(import_dir)
align_files = g.searchdirectory('mRNA_alignments')
reAnalyzeRNAProbesetMatches(align_files, species, array_type,
pairwise_probeset_combinations)
def reformatPolyAdenylationCoordinates(species, force):
""" PolyA annotations are currently only available from UCSC for human, but flat file
annotations from 2003-2006 are available for multiple species. Convert these to BED format"""
version = {}
version['Rn'] = '2003(rn3)'
version['Dr'] = '2003(zv4)'
version['Gg'] = '2004(galGal2)'
version['Hs'] = '2006(hg8)'
version['Mm'] = '2004(mm5)'
print 'Exporting polyADB_2 coordinates as BED for', species
### Obtain the necessary database files
url = 'http://altanalyze.org/archiveDBs/all/polyAsite.txt'
output_dir = 'AltDatabase/ucsc/' + species + '/'
if force == 'yes':
filename, status = update.download(url, output_dir, '')
else:
filename = output_dir + 'polyAsite.txt'
### Import the refseq to Ensembl information
import gene_associations
import OBO_import
import EnsemblImport
import export
try:
ens_unigene = gene_associations.getGeneToUid(species,
'Ensembl-UniGene')
print len(ens_unigene), 'Ensembl-UniGene entries imported'
external_ensembl = OBO_import.swapKeyValues(ens_unigene)
use_entrez = 'no'
except Exception:
ens_entrez = gene_associations.getGeneToUid(species,
'Ensembl-EntrezGene')
print len(ens_entrez), 'Ensembl-EntrezGene entries imported'
external_ensembl = OBO_import.swapKeyValues(ens_entrez)
use_entrez = 'yes'
gene_location_db = EnsemblImport.getEnsemblGeneLocations(
species, 'RNASeq', 'key_by_array')
export_bedfile = output_dir + species + '_polyADB_2_predictions.bed'
print 'exporting', export_bedfile
export_data = export.ExportFile(export_bedfile)
header = '#' + species + '\t' + 'polyADB_2' + '\t' + version[species] + '\n'
export_data.write(header)
fn = filepath(filename)
x = 0
not_found = {}
for line in open(fn, 'rU').xreadlines():
data = cleanUpLine(line)
if x == 0: x = 1
else:
siteid, llid, chr, sitenum, position, supporting_EST, cleavage = string.split(
data, '\t')
if chr == 'chrM':
chr = 'chrMT' ### MT is the Ensembl convention whereas M is the Affymetrix and UCSC convention
if chr == 'M':
chr = 'MT' ### MT is the Ensembl convention whereas M is the Affymetrix and UCSC convention
if species in siteid:
if 'NA' not in chr: chr = 'chr' + chr
strand = '+'
geneid = siteid
pos_start = str(int(position) - 1)
pos_end = position
if use_entrez == 'no':
external_geneid = string.join(
string.split(siteid, '.')[:2], '.')
else:
external_geneid = llid
if external_geneid in external_ensembl:
ens_geneid = external_ensembl[external_geneid][0]
geneid += '-' + ens_geneid
chr, strand, start, end = gene_location_db[ens_geneid]
else:
not_found[external_geneid] = []
bed_format = string.join(
[chr, pos_start, pos_end, geneid, '0', '-'], '\t'
) + '\n' ### We don't know the strand, so write out both strands
export_data.write(bed_format)
bed_format = string.join(
[chr, pos_start, pos_end, geneid, '0', strand],
'\t') + '\n'
export_data.write(bed_format)
export_data.close()
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)
