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 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 command_update(*args):
"""
Update to latest development version
"""
import update
if not (update.download() and update.install()):
print("UPDATE FAILED")
def command_update(*args):
"""
Update to latest development version
"""
import update
if not (update.download() and update.install()):
print("UPDATE FAILED")
def importUCSCTranscriptSequences(species,array_type,probeset_seq_db):
start_time = time.time()
if force == 'yes':
### Download mRNA sequence file from website
import UI; species_names = UI.getSpeciesInfo()
species_full = species_names[species]
species_full = string.replace(species_full,' ','_')
ucsc_mRNA_dir = update.getFTPData('hgdownload.cse.ucsc.edu','/goldenPath/currentGenomes/'+species_full+'/bigZips','mrna.fa.gz')
output_dir = 'AltDatabase/'+species+'/SequenceData/'
try:
gz_filepath, status = update.download(ucsc_mRNA_dir,output_dir,'')
if status == 'not-removed':
try: os.remove(gz_filepath) ### Not sure why this works now and not before
except OSError: status = status
except Exception: null=[] ### Occurs when file is not available for this species
filename = 'AltDatabase/'+species+'/SequenceData/mrna.fa'
output_file = 'AltDatabase/'+species+'/SequenceData/output/'+array_type+'_UCSC-mRNA_alignments.txt'
dataw = export.ExportFile(output_file)
output_file = 'AltDatabase/'+species+'/SequenceData/output/sequences/'+array_type+'_UCSC_mRNA_seqmatches.txt'
datar = export.ExportFile(output_file)
ucsc_mrna_to_gene = importUCSCTranscriptAssociations(species)
print "Begining generic fasta import of",filename
#'>gnl|ENS|Mm#S10859962 Mus musculus 12 days embryo spinal ganglion cDNA /gb=AK051143 /gi=26094349 /ens=Mm.1 /len=2289']
#'ATCGTGGTGTGCCCAGCTCTTCCAAGGACTGCTGCGCTTCGGGGCCCAGGTGAGTCCCGC'
fn=filepath(filename); sequence = '|'; ucsc_mRNA_hit_len={}; ucsc_probeset_null_hits={}; k=0
fn=filepath(filename); sequence = '|'; ucsc_mRNA_hit_len={}; ucsc_probeset_null_hits={}; k=0
for line in open(fn,'rU').xreadlines():
try: data, newline= string.split(line,'\n')
except ValueError: continue
if len(data)>0:
if data[0] != '#':
try:
if data[0] == '>':
if len(sequence) > 1:
if accession in ucsc_mrna_to_gene:
gene_found = 'no'
for ens_gene in ucsc_mrna_to_gene[accession]:
if ens_gene in probeset_seq_db:
sequence = string.upper(sequence); gene_found = 'yes'
mRNA_seq = sequence[1:]; mRNA_length = len(mRNA_seq)
k+=1; probeset_seq_data = probeset_seq_db[ens_gene]
results = simpleSeqMatchProtocol(probeset_seq_data,mRNA_seq)
for (call,probeset) in results:
dataw.write(string.join([probeset,str(call),accession],'\t')+'\n')
if gene_found == 'yes':
values = [accession,mRNA_seq]; values = string.join(values,'\t')+'\n'
datar.write(values)
values = string.split(data,' '); accession = values[0][1:]
sequence = '|'; continue
except IndexError: null = []
try:
if data[0] != '>': sequence = sequence + data
except IndexError: print kill; continue
datar.close()
end_time = time.time(); time_diff = int(end_time-start_time)
print "UCSC mRNA sequences analyzed in %d seconds" % time_diff
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 importmiRNAMap(parse_sequences,force):
""" Added in AltAnalyze version 2.0, this database provides target sequences for several species and different databases,
including miRanda, RNAhybrid and TargetScan. For more information see: http://mirnamap.mbc.nctu.edu.tw/html/about.html"""
gz_filepath = verifyFileAdvanced('miRNA_targets_',species)
if force == 'yes' or len(gz_filepath)==0:
import UI; species_names = UI.getSpeciesInfo()
species_full = species_names[species]
species_full = string.replace(species_full,' ','_')
miRNAMap_dir = update.getFTPData('mirnamap.mbc.nctu.edu.tw','/miRNAMap2/miRNA_Targets/'+species_full,'.txt.tar.gz')
output_dir = 'AltDatabase/miRBS/'+species+'/'
gz_filepath, status = update.download(miRNAMap_dir,output_dir,'')
if status == 'not-removed':
try: os.remove(gz_filepath) ### Not sure why this works now and not before
except OSError: status = status
fn=filepath(string.replace(gz_filepath,'.tar.gz','')); x=0; count=0
for line in open(fn,'rU').readlines():
data = cleanUpLine(line)
t = string.split(data,'\t')
if x==0: x=1
else:
try:
miRNA, ensembl_transcript_id, target_start, target_end, miRNA_seq, alignment, target_seq, algorithm, c1, c2, c3 = t
#if 'GGCTCCTGTCACCTGGGTCCGT'in target_seq:
#print 'a'; sys.exit()
#if 'TCF7L1' in symbol or 'TCF3' in symbol:
#if '-422a' in miRNA:
#print miRNA;sys.exit()
#print symbol, mir; sys.exit()
if ensembl_transcript_id in ens_gene_to_transcript:
geneids = ens_gene_to_transcript[ensembl_transcript_id]
target_seq = string.upper(string.replace(target_seq,'-',''))
target_seq = string.replace(target_seq,'U','T')
for ensembl_geneid in geneids:
if parse_sequences == 'yes':
if (miRNA,ensembl_geneid) in combined_results:
combined_results[(miRNA,ensembl_geneid)].append(target_seq)
else:
y = MicroRNATargetData(ensembl_geneid,'',miRNA,target_seq,algorithm); count+=1
try: microRNA_target_db[miRNA].append(y)
except KeyError: microRNA_target_db[miRNA] = [y]
except Exception: x=1 ### Bad formatting
print count, 'miRNA-target relationships added for mirnamap'
return count
def downloadFile(file_type):
import UI
file_location_defaults = UI.importDefaultFileLocations()
try:
fld = file_location_defaults[file_type]
url = fld.Location()
except Exception:
for fl in fld:
if species in fl.Species(): url = fl.Location()
if 'Target' in file_type: output_dir = 'AltDatabase/miRBS/'
else: output_dir = 'AltDatabase/miRBS/'+species + '/'
gz_filepath, status = update.download(url,output_dir,'')
if status == 'not-removed':
try: os.remove(gz_filepath) ### Not sure why this works now and not before
except Exception: status = status
filename = string.replace(gz_filepath,'.zip','.txt')
filename = string.replace(filename,'.gz','.txt')
filename = string.replace(filename,'.txt.txt','.txt')
return filename
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()
import update
passive_partition = update.get_passive_partition()
print(passive_partition)
def progress_callback(percentage):
print(percentage)
update.download(url='https://github.com/wipfli/update/releases/download/v0.1.0/rootfs.ext2.xz', passive_partition=passive_partition, progress_callback=progress_callback, total_size=52807640)
print(update.get_checksum(passive_partition))
update.flash_boot_select(passive_partition)
def download_updates(self):
now = int(time.mktime(time.gmtime()))
if now > settings.server.get('last_update_check', 0) + 24*60*60:
settings.server['last_update_check'] = now
update.download()
### Update password crypt
if currentVersion<2050:
MessageBox(None, u'Vous devez reconfigurer le Bot !', u'update', 0)
updatef = zipfile.ZipFile('./config_original.zip')
updatef.extractall()
### Get config Gui
try:
os.chdir(os.path.dirname(sys.argv[0]))
except:
pass
if currentVersion<3001 or not os.path.exists('config.exe'):
download('https://github.com/downloads/maxisoft/millenium-bot/config.exe','config.exe')
### ----------------- restart le service
try:
RunCMD('sc start "MillenuimBot"')
except:
pass
### Retour au repertoir de depart
try:
os.chdir(os.path.dirname(sys.argv[0]))
except:
pass
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 importUCSCTranscriptSequences(species, array_type, probeset_seq_db):
start_time = time.time()
if force == 'yes':
### Download mRNA sequence file from website
import UI
species_names = UI.getSpeciesInfo()
species_full = species_names[species]
species_full = string.replace(species_full, ' ', '_')
ucsc_mRNA_dir = update.getFTPData(
'hgdownload.cse.ucsc.edu',
'/goldenPath/currentGenomes/' + species_full + '/bigZips',
'mrna.fa.gz')
output_dir = 'AltDatabase/' + species + '/SequenceData/'
try:
gz_filepath, status = update.download(ucsc_mRNA_dir, output_dir,
'')
if status == 'not-removed':
try:
os.remove(gz_filepath
) ### Not sure why this works now and not before
except OSError:
status = status
except Exception:
null = [] ### Occurs when file is not available for this species
filename = 'AltDatabase/' + species + '/SequenceData/mrna.fa'
output_file = 'AltDatabase/' + species + '/SequenceData/output/' + array_type + '_UCSC-mRNA_alignments.txt'
dataw = export.ExportFile(output_file)
output_file = 'AltDatabase/' + species + '/SequenceData/output/sequences/' + array_type + '_UCSC_mRNA_seqmatches.txt'
datar = export.ExportFile(output_file)
ucsc_mrna_to_gene = importUCSCTranscriptAssociations(species)
print "Begining generic fasta import of", filename
#'>gnl|ENS|Mm#S10859962 Mus musculus 12 days embryo spinal ganglion cDNA /gb=AK051143 /gi=26094349 /ens=Mm.1 /len=2289']
#'ATCGTGGTGTGCCCAGCTCTTCCAAGGACTGCTGCGCTTCGGGGCCCAGGTGAGTCCCGC'
fn = filepath(filename)
sequence = '|'
ucsc_mRNA_hit_len = {}
ucsc_probeset_null_hits = {}
k = 0
fn = filepath(filename)
sequence = '|'
ucsc_mRNA_hit_len = {}
ucsc_probeset_null_hits = {}
k = 0
for line in open(fn, 'rU').xreadlines():
try:
data, newline = string.split(line, '\n')
except ValueError:
continue
if len(data) > 0:
if data[0] != '#':
try:
if data[0] == '>':
if len(sequence) > 1:
if accession in ucsc_mrna_to_gene:
gene_found = 'no'
for ens_gene in ucsc_mrna_to_gene[accession]:
if ens_gene in probeset_seq_db:
sequence = string.upper(sequence)
gene_found = 'yes'
mRNA_seq = sequence[1:]
mRNA_length = len(mRNA_seq)
k += 1
probeset_seq_data = probeset_seq_db[
ens_gene]
results = simpleSeqMatchProtocol(
probeset_seq_data, mRNA_seq)
for (call, probeset) in results:
dataw.write(
string.join([
probeset,
str(call), accession
], '\t') + '\n')
if gene_found == 'yes':
values = [accession, mRNA_seq]
values = string.join(values, '\t') + '\n'
datar.write(values)
values = string.split(data, ' ')
accession = values[0][1:]
sequence = '|'
continue
except IndexError:
null = []
try:
if data[0] != '>': sequence = sequence + data
except IndexError:
print kill
continue
datar.close()
end_time = time.time()
time_diff = int(end_time - start_time)
print "UCSC mRNA sequences analyzed in %d seconds" % time_diff
def importUCSCTranscriptSequences(species, array_type, probeset_seq_db):
start_time = time.time()
if force == "yes":
### Download mRNA sequence file from website
import UI
species_names = UI.getSpeciesInfo()
species_full = species_names[species]
species_full = string.replace(species_full, " ", "_")
ucsc_mRNA_dir = update.getFTPData(
"hgdownload.cse.ucsc.edu", "/goldenPath/currentGenomes/" + species_full + "/bigZips", "mrna.fa.gz"
)
output_dir = "AltDatabase/" + species + "/SequenceData/"
try:
gz_filepath, status = update.download(ucsc_mRNA_dir, output_dir, "")
if status == "not-removed":
try:
os.remove(gz_filepath) ### Not sure why this works now and not before
except OSError:
status = status
except Exception:
null = [] ### Occurs when file is not available for this species
filename = "AltDatabase/" + species + "/SequenceData/mrna.fa"
output_file = "AltDatabase/" + species + "/SequenceData/output/" + array_type + "_UCSC-mRNA_alignments.txt"
dataw = export.ExportFile(output_file)
output_file = (
"AltDatabase/" + species + "/SequenceData/output/sequences/" + array_type + "_UCSC_mRNA_seqmatches.txt"
)
datar = export.ExportFile(output_file)
ucsc_mrna_to_gene = importUCSCTranscriptAssociations(species)
print "Begining generic fasta import of", filename
#'>gnl|ENS|Mm#S10859962 Mus musculus 12 days embryo spinal ganglion cDNA /gb=AK051143 /gi=26094349 /ens=Mm.1 /len=2289']
#'ATCGTGGTGTGCCCAGCTCTTCCAAGGACTGCTGCGCTTCGGGGCCCAGGTGAGTCCCGC'
fn = filepath(filename)
sequence = "|"
ucsc_mRNA_hit_len = {}
ucsc_probeset_null_hits = {}
k = 0
fn = filepath(filename)
sequence = "|"
ucsc_mRNA_hit_len = {}
ucsc_probeset_null_hits = {}
k = 0
for line in open(fn, "rU").xreadlines():
try:
data, newline = string.split(line, "\n")
except ValueError:
continue
if len(data) > 0:
if data[0] != "#":
try:
if data[0] == ">":
if len(sequence) > 1:
if accession in ucsc_mrna_to_gene:
gene_found = "no"
for ens_gene in ucsc_mrna_to_gene[accession]:
if ens_gene in probeset_seq_db:
sequence = string.upper(sequence)
gene_found = "yes"
mRNA_seq = sequence[1:]
mRNA_length = len(mRNA_seq)
k += 1
probeset_seq_data = probeset_seq_db[ens_gene]
results = simpleSeqMatchProtocol(probeset_seq_data, mRNA_seq)
for (call, probeset) in results:
dataw.write(string.join([probeset, str(call), accession], "\t") + "\n")
if gene_found == "yes":
values = [accession, mRNA_seq]
values = string.join(values, "\t") + "\n"
datar.write(values)
values = string.split(data, " ")
accession = values[0][1:]
sequence = "|"
continue
except IndexError:
null = []
try:
if data[0] != ">":
sequence = sequence + data
except IndexError:
print kill
continue
datar.close()
end_time = time.time()
time_diff = int(end_time - start_time)
print "UCSC mRNA sequences analyzed in %d seconds" % time_diff
def downloadHMDBMetaboCardFlatFile():
url = 'http://www.hmdb.ca/public/downloads/current/metabocards.zip'
fln, status = update.download(url, 'BuildDBs/HMDB/', '')
def downloadKEGGPathwayIDs():
url = 'ftp://ftp.genome.jp/pub/kegg/pathway/map_title.tab'
fln, status = update.download(url, 'BuildDBs/HMDB/', '')
def download_updates(self):
now = int(time.mktime(time.gmtime()))
if now > settings.server.get('last_update_check', 0) + 24 * 60 * 60:
settings.server['last_update_check'] = now
update.download()