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 runExtractUniProt(species,species_full,uniprot_filename_url,trembl_filename_url,force):
    global uniprot_ensembl_db;uniprot_ensembl_db={}
    global uniprot_db;uniprot_db={}; global species_name; global uniprot_fildir
    global secondary_to_primary_db; secondary_to_primary_db={}
    import update; reload(update)
    
    species_name = species_full
    
    import UI; species_names = UI.getSpeciesInfo()
    species_full = species_names[species]
    species_full = string.replace(species_full,' ','_')

    uniprot_file = string.split(uniprot_filename_url,'/')[-1]; uniprot_file = string.replace(uniprot_file,'.gz','')
    trembl_file = string.split(trembl_filename_url,'/')[-1]; trembl_file = string.replace(trembl_file,'.gz','')
    uniprot_fildir = 'AltDatabase/uniprot/'+species+'/'
    uniprot_download_fildir = 'AltDatabase/uniprot/'
    uniprot_ens_file = species+'_Ensembl-UniProt.txt'; uniprot_ens_location = uniprot_fildir+uniprot_ens_file
    uniprot_location = uniprot_download_fildir+uniprot_file
    trembl_location = uniprot_download_fildir+trembl_file

    add_trembl_annotations = 'no' ### Currently we don't need these annotations    
    try: importEnsemblUniprot(uniprot_ens_location)
    except IOError:
        try:
            ### Download the data from the AltAnalyze website (if there)
            update.downloadCurrentVersion(uniprot_ens_location,species,'txt')
            importEnsemblUniprot(uniprot_ens_location)
        except Exception: null=[]
    try:
        uniprot_ens_location_built = string.replace(uniprot_ens_location,'UniProt','Uniprot-SWISSPROT')
        uniprot_ens_location_built = string.replace(uniprot_ens_location_built,'uniprot','Uniprot-SWISSPROT')
        importEnsemblUniprot(uniprot_ens_location_built)
    except Exception: null=[]
    
    ### Import UniProt annotations
    counts = update.verifyFile(uniprot_location,'counts')
    if force == 'no' or counts > 8: import_uniprot_db(uniprot_location)
    else:
        ### Directly download the data from UniProt
        gz_filepath, status = update.download(uniprot_filename_url,uniprot_download_fildir,'')

        if status == 'not-removed':
            try: os.remove(gz_filepath) ### Not sure why this works now and not before
            except OSError: status = status     
        import_uniprot_db(uniprot_location)
        
    if add_trembl_annotations == 'yes':
        ### Import TreMBL annotations
        try:
            if force == 'yes': uniprot_location += '!!!!!' ### Force an IOError
            import_uniprot_db(trembl_location)
        except IOError:
            ### Directly download the data from UniProt
            update.download(trembl_filename_url,uniprot_download_fildir,'')
            import_uniprot_db(trembl_location)        
    export()
    exportEnsemblUniprot(uniprot_ens_location)
Exemple #3
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def runExtractUniProt(species,species_full,uniprot_filename_url,trembl_filename_url,force):
    global uniprot_ensembl_db;uniprot_ensembl_db={}
    global uniprot_db;uniprot_db={}; global species_name; global uniprot_fildir
    global secondary_to_primary_db; secondary_to_primary_db={}
    import update; reload(update)
    
    species_name = species_full
    
    import UI; species_names = UI.getSpeciesInfo()
    species_full = species_names[species]
    species_full = string.replace(species_full,' ','_')

    uniprot_file = string.split(uniprot_filename_url,'/')[-1]; uniprot_file = string.replace(uniprot_file,'.gz','')
    trembl_file = string.split(trembl_filename_url,'/')[-1]; trembl_file = string.replace(trembl_file,'.gz','')
    uniprot_fildir = 'AltDatabase/uniprot/'+species+'/'
    uniprot_download_fildir = 'AltDatabase/uniprot/'
    uniprot_ens_file = species+'_Ensembl-UniProt.txt'; uniprot_ens_location = uniprot_fildir+uniprot_ens_file
    uniprot_location = uniprot_download_fildir+uniprot_file
    trembl_location = uniprot_download_fildir+trembl_file

    add_trembl_annotations = 'no' ### Currently we don't need these annotations    
    try: importEnsemblUniprot(uniprot_ens_location)
    except IOError:
        try:
            ### Download the data from the AltAnalyze website (if there)
            update.downloadCurrentVersion(uniprot_ens_location,species,'txt')
            importEnsemblUniprot(uniprot_ens_location)
        except Exception: null=[]
    try:
        uniprot_ens_location_built = string.replace(uniprot_ens_location,'UniProt','Uniprot-SWISSPROT')
        uniprot_ens_location_built = string.replace(uniprot_ens_location_built,'uniprot','Uniprot-SWISSPROT')
        importEnsemblUniprot(uniprot_ens_location_built)
    except Exception: null=[]
    
    ### Import UniProt annotations
    counts = update.verifyFile(uniprot_location,'counts')
    if force == 'no' or counts > 8: import_uniprot_db(uniprot_location)
    else:
        ### Directly download the data from UniProt
        gz_filepath, status = update.download(uniprot_filename_url,uniprot_download_fildir,'')

        if status == 'not-removed':
            try: os.remove(gz_filepath) ### Not sure why this works now and not before
            except OSError: status = status     
        import_uniprot_db(uniprot_location)
        
    if add_trembl_annotations == 'yes':
        ### Import TreMBL annotations
        try:
            if force == 'yes': uniprot_location += '!!!!!' ### Force an IOError
            import_uniprot_db(trembl_location)
        except IOError:
            ### Directly download the data from UniProt
            update.download(trembl_filename_url,uniprot_download_fildir,'')
            import_uniprot_db(trembl_location)        
    export()
    exportEnsemblUniprot(uniprot_ens_location)
def checkProbesetSequenceFile(species):
    """ Check to see if the probeset sequence file is present and otherwise download AltAnalyze hosted version"""
    probeset_seq_file = getProbesetSequenceFile(species)
    if probeset_seq_file == None:
        dir = '/AltDatabase/'+species+'/'+array_type
        filename = update.getFileLocations(species,'exon_seq')
        filename = dir[1:]+'/'+ filename
        update.downloadCurrentVersion(filename,'exon','.fa')
        probeset_seq_file = getProbesetSequenceFile(species)
    return probeset_seq_file
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
Exemple #6
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def verifyFile(filename,species_name):
    fn=filepath(filename); counts=0
    try:
        for line in open(fn,'rU').xreadlines():
            counts+=1
            if counts>10: break
    except Exception:
        counts=0
    if species_name == 'counts': ### Used if the file cannot be downloaded from http://www.altanalyze.org
        return counts
    elif counts == 0:
        if species_name in filename: server_folder = species_name ### Folder equals species unless it is a universal file
        elif 'Mm' in filename: server_folder = 'Mm' ### For PicTar
        else: server_folder = 'all'
        print 'Downloading:',server_folder,filename
        update.downloadCurrentVersion(filename,server_folder,'txt')
    else:
        return counts
def verifyFile(filename, species_name):
    fn = filepath(filename)
    counts = 0
    try:
        for line in open(fn, 'rU').xreadlines():
            counts += 1
            if counts > 10: break
    except Exception:
        counts = 0
    if species_name == 'counts':  ### Used if the file cannot be downloaded from http://www.altanalyze.org
        return counts
    elif counts == 0:
        if species_name in filename:
            server_folder = species_name  ### Folder equals species unless it is a universal file
        elif 'Mm' in filename:
            server_folder = 'Mm'  ### For PicTar
        else:
            server_folder = 'all'
        print 'Downloading:', server_folder, filename
        update.downloadCurrentVersion(filename, server_folder, 'txt')
    else:
        return counts