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 importSplicingAnnotationDatabaseAndSequence(species,array_type,biotype):
array_ens_db={}
if array_type == 'AltMouse':
filename = 'AltDatabase/'+species+'/'+array_type+'/'+array_type+'-Ensembl_relationships.txt'
update.verifyFile(filename,array_type) ### Will force download if missing
fn=filepath(filename); x = 0
for line in open(fn,'r').xreadlines():
data, newline = string.split(line,'\n'); t = string.split(data,'\t')
if x==0: x=1
else:
array_gene,ens_gene = t
try: array_ens_db[array_gene].append(ens_gene)
except KeyError: array_ens_db[array_gene]=[ens_gene]
filename = 'AltDatabase/'+species+'/'+array_type+'/'+array_type+'_critical-junction-seq.txt'
fn=filepath(filename); probeset_seq_db={}; x = 0
for line in open(fn,'r').xreadlines():
data, newline = string.split(line,'\n'); t = string.split(data,'\t')
if x==0: x=1
else:
probeset,probeset_seq,junction_seq = t; junction_seq=string.replace(junction_seq,'|','')
probeset_seq_db[probeset] = probeset_seq,junction_seq
###Import reciprocol junctions, so we can compare these directly instead of hits to nulls and combine with sequence data
###This short-cuts what we did in two function in ExonSeqModule with exon level data
filename = 'AltDatabase/'+species+'/'+array_type+'/'+array_type+'_junction-comparisons.txt'
fn=filepath(filename); probeset_gene_seq_db={}; x = 0
for line in open(fn,'r').xreadlines():
data, newline = string.split(line,'\n'); t = string.split(data,'\t')
if x==0: x=1
else:
array_gene,probeset1,probeset2,critical_exons = t #; critical_exons = string.split(critical_exons,'|')
probesets = [probeset1,probeset2]
if array_type == 'junction' or array_type == 'RNASeq': array_ens_db[array_gene]=[array_gene]
if array_gene in array_ens_db:
ensembl_gene_ids = array_ens_db[array_gene]
for probeset_id in probesets:
if probeset_id in probeset_seq_db:
probeset_seq,junction_seq = probeset_seq_db[probeset_id]
if biotype == 'gene':
for ensembl_gene_id in ensembl_gene_ids:
probe_data = ExonSeqModule.JunctionDataSimple(probeset_id,ensembl_gene_id,array_gene,probesets,critical_exons)
probe_data.SetExonSeq(probeset_seq)
probe_data.SetJunctionSeq(junction_seq)
try: probeset_gene_seq_db[ensembl_gene_id].append(probe_data)
except KeyError: probeset_gene_seq_db[ensembl_gene_id] = [probe_data]
else: ### Used for probeset annotations downstream of sequence alignment in LinkEST, analagous to exon_db for exon analyses
probe_data = ExonSeqModule.JunctionDataSimple(probeset_id,ensembl_gene_ids,array_gene,probesets,critical_exons)
probe_data.SetExonSeq(probeset_seq)
probe_data.SetJunctionSeq(junction_seq)
probeset_gene_seq_db[probeset_id] = probe_data
print len(probeset_gene_seq_db),"genes with probeset sequence associated"
return probeset_gene_seq_db
def getParametersAndExecute(probeset_seq_file,array_type,species,data_type):
if data_type == 'critical-exons':
if array_type == 'RNASeq': probeset_annotations_file = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_Ensembl_exons.txt'
else: probeset_annotations_file = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_Ensembl_'+array_type+'_probesets.txt'
###Import probe-level associations
exon_db = ExonSeqModule.importSplicingAnnotationDatabase(probeset_annotations_file,array_type)
start_time = time.time()
probeset_seq_db = importProbesetSeqeunces(probeset_seq_file,exon_db,species) ###Do this locally with a function that works on tab-delimited as opposed to fasta sequences (exon array)
end_time = time.time(); time_diff = int(end_time-start_time)
elif data_type == 'junctions':
start_time = time.time(); biotype = 'gene' ### Indicates whether to store information at the level of genes or probesets
probeset_seq_db = importSplicingAnnotationDatabaseAndSequence(species,array_type,biotype)
end_time = time.time(); time_diff = int(end_time-start_time)
print "Analyses finished in %d seconds" % time_diff
return probeset_seq_db
def executeParameters(species,array_type,force,genomic_build,update_uniprot,update_ensembl,update_probeset_to_ensembl,update_domain,update_miRs,update_all,update_miR_seq,ensembl_version):
if '|' in array_type: array_type, specific_array_type = string.split(array_type,'|') ### To destinguish between array sub-types, like the HJAY and hGlue
else: specific_array_type = array_type
if update_all == 'yes':
update_uniprot='yes'; update_ensembl='yes'; update_probeset_to_ensembl='yes'; update_domain='yes'; update_miRs = 'yes'
if update_ensembl == 'yes':
from build_scripts import EnsemblSQL; reload(EnsemblSQL)
""" Used to grab all essential Ensembl annotations previously obtained via BioMart"""
configType = 'Advanced'; analysisType = 'AltAnalyzeDBs'; externalDBName = ''
EnsemblSQL.buildEnsemblRelationalTablesFromSQL(species,configType,analysisType,externalDBName,ensembl_version,force)
""" Used to grab Ensembl-to-External gene associations"""
configType = 'Basic'; analysisType = 'ExternalOnly'; externalDBName = 'Uniprot/SWISSPROT'
EnsemblSQL.buildEnsemblRelationalTablesFromSQL(species,configType,analysisType,externalDBName,ensembl_version,force)
""" Used to grab Ensembl full gene sequence plus promoter and 3'UTRs """
if array_type == 'AltMouse' or array_type == 'junction' or array_type == 'RNASeq':
EnsemblSQL.getFullGeneSequences(ensembl_version,species)
if update_uniprot == 'yes':
###Might need to delete the existing versions of downloaded databases or force download
buildUniProtFunctAnnotations(species,force)
if update_probeset_to_ensembl == 'yes':
if species == 'Mm' and array_type == 'AltMouse':
buildAltMouseExonAnnotations(species,array_type,force,genomic_build)
elif array_type == 'junction':
buildJunctionExonAnnotations(species,array_type,specific_array_type,force,genomic_build)
elif array_type == 'RNASeq':
import RNASeq; test_status = 'no'; data_type = 'mRNA'
RNASeq.getEnsemblAssociations(species,data_type,test_status,force)
else: buildExonArrayExonAnnotations(species,array_type,force)
if update_domain == 'yes':
if array_type == 'RNASeq':
only_rely_on_coordinate_mapping = True ### This will provide more accurate results as many junctions have missing sequences
else:
only_rely_on_coordinate_mapping = False
from build_scripts import FeatureAlignment
from build_scripts import JunctionArray
from build_scripts import mRNASeqAlign
from build_scripts import IdentifyAltIsoforms
### Get UCSC associations for all Ensembl linked genes (download databases if necessary) if species == 'Mm' and array_type == 'AltMouse':
mRNA_Type = 'mrna'; run_from_scratch = 'yes'
export_all_associations = 'yes' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species,mRNA_Type,export_all_associations,run_from_scratch,force)
if (species == 'Mm' and array_type == 'AltMouse'):
"""Imports and re-exports array-Ensembl annotations"""
null = JunctionArray.importArrayAnnotations(species,array_type); null={}
if (species == 'Mm' and array_type == 'AltMouse') or array_type == 'junction' or array_type == 'RNASeq':
if only_rely_on_coordinate_mapping == False:
"""Performs probeset sequence aligment to Ensembl and UCSC transcripts. To do: Need to setup download if files missing"""
analysis_type = 'reciprocal'
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,analysis_type,force)
run_seqcomp = 'no'
if only_rely_on_coordinate_mapping == False:
IdentifyAltIsoforms.runProgram(species,array_type,'null',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'null')
if array_type == 'junction' or array_type == 'RNASeq':
if only_rely_on_coordinate_mapping == False:
### For junction probeset sequences from mRNASeqAlign(), find and assess alternative proteins - export to the folder 'junction'
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,'single',force)
IdentifyAltIsoforms.runProgram(species,array_type,'junction',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'junction')
### For exon probesets (and junction exons) align and assess alternative proteins - export to the folder 'exon'
IdentifyAltIsoforms.runProgram(species,array_type,'exon',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'exon') # not needed
""" Repeat above with CoordinateBasedMatching = True """
### Peform coordinate based junction mapping to transcripts (requires certain sequence files built in IdentifyAltIosofmrs)
analysis_type = 'reciprocal'
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,analysis_type,force,CoordinateBasedMatching = True)
IdentifyAltIsoforms.runProgram(species,array_type,'null',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'null')
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,'single',force,CoordinateBasedMatching = True)
IdentifyAltIsoforms.runProgram(species,array_type,'junction',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'junction')
IdentifyAltIsoforms.runProgram(species,array_type,'exon',force,run_seqcomp)
if array_type == 'RNASeq':
JunctionArray.combineExonJunctionAnnotations(species,array_type)
if update_miRs == 'yes':
if update_miR_seq == 'yes':
from build_scripts import MatchMiRTargetPredictions; only_add_sequence_to_previous_results = 'no'
MatchMiRTargetPredictions.runProgram(species,force,only_add_sequence_to_previous_results)
if array_type == 'exon' or array_type == 'gene':
from build_scripts import ExonSeqModule
stringency = 'strict'; process_microRNA_predictions = 'yes'; mir_source = 'multiple'
ExonSeqModule.runProgram(species,array_type,process_microRNA_predictions,mir_source,stringency)
stringency = 'lax'
ExonSeqModule.runProgram(species,array_type,process_microRNA_predictions,mir_source,stringency)
ExonArray.exportMetaProbesets(array_type,species) ### Export metaprobesets for this build
else:
from build_scripts import JunctionSeqModule
stringency = 'strict'; mir_source = 'multiple'
JunctionSeqModule.runProgram(species,array_type,mir_source,stringency,force)
stringency = 'lax'
JunctionSeqModule.runProgram(species,array_type,mir_source,stringency,force)
if array_type == 'junction':
try:
from build_scripts import JunctionArray; from build_scripts import JunctionArrayEnsemblRules
JunctionArray.filterForCriticalExons(species,array_type)
JunctionArray.overRideExonEntriesWithJunctions(species,array_type)
JunctionArrayEnsemblRules.annotateJunctionIDsAsExon(species,array_type)
ExonArray.exportMetaProbesets(array_type,species) ### Export metaprobesets for this build
except IOError: print 'No built junction files to analyze';sys.exit()
if array_type == 'RNASeq' and (species == 'Hs' or species == 'Mm' or species == 'Rn'):
from build_scripts import JunctionArray; from build_scripts import JunctionArrayEnsemblRules
try: JunctionArrayEnsemblRules.annotateJunctionIDsAsExon(species,array_type)
except IOError: print 'No Ensembl_exons.txt file to analyze';sys.exit()
try:
filename = 'AltDatabase/'+species+'/SequenceData/miRBS-combined_gene-targets.txt'; ef=filepath(filename)
er = string.replace(ef,species+'/SequenceData/miRBS-combined_gene-targets.txt','ensembl/'+species+'/'+species+'_microRNA-Ensembl.txt')
import shutil; shutil.copyfile(ef,er)
except Exception: null=[]
if array_type != 'RNASeq':
### Get the probeset-probe relationships from online - needed for FIRMA analysis
filename = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_probeset-probes.txt'
if array_type == 'junction' and 'lue' in specific_array_type:
server_folder = 'junction/hGlue'
verifyFile(filename,server_folder) ### Will force download if missing
verifyFile('AltDatabase/'+species+'/'+array_type+'/platform.txt',server_folder) ### Will force download if missing
elif array_type != 'AltMouse': verifyFile(filename,array_type) ### Will force download if missing
if (array_type == 'exon' or array_type == 'AltMouse') and species != 'Rn':
try:
### Available for select exon-arrays and AltMouse
probeset_to_remove_file = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_probes_to_remove.txt'
verifyFile(probeset_to_remove_file,array_type)
except Exception: null=[]
def annotateJunctionIDsAsExon(species, array_type):
from build_scripts import ExonSeqModule
probeset_annotations_file = 'AltDatabase/' + species + '/' + array_type + '/' + species + '_Ensembl_junction_probesets-filtered.txt'
if array_type == 'RNASeq':
probeset_annotations_file = string.replace(
probeset_annotations_file, 'junction_probesets-filtered', 'exons')
junction_exon_db = ExonSeqModule.importSplicingAnnotationDatabase(
probeset_annotations_file, array_type)
probeset_annotations_file = 'AltDatabase/' + species + '/exon/' + species + '_Ensembl_probesets.txt'
exon_db = ExonSeqModule.importSplicingAnnotationDatabase(
probeset_annotations_file, array_type)
### Extract unique exon regions from Exon Array annotations
multiple_exon_regions = {}
unique_exon_regions = {}
for probeset in exon_db:
y = exon_db[probeset]
geneid = y.GeneID()
if '|' in y.ExonRegionID():
exonids = string.split(y.ExonRegionID(), '|')
for exonid in exonids:
multiple_exon_regions[geneid, exonid] = y
else:
unique_exon_regions[geneid, y.ExonRegionID()] = y
### Add missing exons to unique
for uid in multiple_exon_regions:
if uid not in unique_exon_regions:
unique_exon_regions[uid] = multiple_exon_regions[uid]
"""
for i in unique_exon_regions:
if 'ENSMUSG00000066842' in i:
print i
stop
"""
### Extract unique exon regions from Junction Array annotation
junction_to_exonids = {}
for probeset in junction_exon_db:
if 'ENSMUSG00000066842' in probeset: print probeset
y = junction_exon_db[probeset]
geneid = y.GeneID()
if '|' in y.ExonRegionID():
exonids = string.split(y.ExonRegionID(), '|')
if probeset == 'ENSMUSG00000066842|E60.1': print[[exonids]]
for exonid in exonids:
if (geneid, exonid) in unique_exon_regions:
y = unique_exon_regions[geneid, exonid]
if probeset == 'ENSMUSG00000066842:E60.1':
print[y.Probeset()]
junction_to_exonids[probeset] = y.Probeset()
else:
if (geneid, string.replace(y.ExonRegionID(), '.',
'-')) in unique_exon_regions:
#if ':' in probeset: print [probeset,y.ExonRegionID()];kill
y = unique_exon_regions[
geneid, string.replace(y.ExonRegionID(), '.', '-')]
junction_to_exonids[probeset] = y.Probeset()
output_file = 'AltDatabase/' + species + '/' + array_type + '/' + species + '_' + array_type + '-exon_probesets.txt'
fn = filepath(output_file)
data = open(fn, 'w')
data.write(array_type + '_probeset\texon_probeset\n')
for probeset in junction_to_exonids:
exon_probeset = junction_to_exonids[probeset]
data.write(probeset + '\t' + exon_probeset + '\n')
data.close()