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':
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':
### 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"""
import JunctionArray
null = JunctionArray.importArrayAnnotations(species,array_type); null={}
if (species == 'Mm' and array_type == 'AltMouse') or array_type == 'junction' or array_type == 'RNASeq':
"""Performs probeset sequence aligment to Ensembl and UCSC transcripts. To do: Need to setup download if files missing"""
import mRNASeqAlign; analysis_type = 'reciprocal'
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,analysis_type,force)
import IdentifyAltIsoforms; run_seqcomp = 'no'
IdentifyAltIsoforms.runProgram(species,array_type,'null',force,run_seqcomp)
import FeatureAlignment; import JunctionArray
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'null')
if array_type == 'junction' or array_type == 'RNASeq':
### 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':
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':
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:
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:
import JunctionArray; 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'):
import JunctionArray; 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 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':
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':
### 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"""
import JunctionArray
null = JunctionArray.importArrayAnnotations(species, array_type)
null = {}
if (species == 'Mm' and array_type == 'AltMouse'
) or array_type == 'junction' or array_type == 'RNASeq':
"""Performs probeset sequence aligment to Ensembl and UCSC transcripts. To do: Need to setup download if files missing"""
import mRNASeqAlign
analysis_type = 'reciprocal'
mRNASeqAlign.alignProbesetsToTranscripts(species, array_type,
analysis_type, force)
import IdentifyAltIsoforms
run_seqcomp = 'no'
IdentifyAltIsoforms.runProgram(species, array_type, 'null', force,
run_seqcomp)
import FeatureAlignment
FeatureAlignment.findDomainsByGenomeCoordinates(
species, array_type, 'null')
if array_type == 'junction' or array_type == 'RNASeq':
### 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')
if array_type == 'junction' or array_type == 'RNASeq':
### 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
if array_type == 'RNASeq':
import JunctionArray
JunctionArray.combineExonJunctionAnnotations(
species, array_type)
if update_miRs == 'yes':
if update_miR_seq == 'yes':
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':
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:
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:
import JunctionArray
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'):
import JunctionArray
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 = []
