def buildUCSCAnnoationFiles(species,mRNA_Type,export_all_associations,run_from_scratch,force):
### Test whether files already exist and if not downloads/builds them
if export_all_associations == 'no': ### Applies to EnsemblImport.py analyses
filename = 'AltDatabase/ucsc/'+species+'/'+species+'_UCSC_transcript_structure_mrna.txt'
else: ### Applies to the file used for Domain-level analyses
filename = 'AltDatabase/ucsc/'+species+'/'+species+'_UCSC_transcript_structure_COMPLETE-mrna.txt'
counts = verifyFile(filename,'counts')
if counts<9:
import UCSCImport
try: UCSCImport.runUCSCEnsemblAssociations(species,mRNA_Type,export_all_associations,run_from_scratch,force)
except Exception: UCSCImport.exportNullDatabases(species) ### used for species not supported by UCSC
def buildUCSCAnnoationFiles(species, mRNA_Type, export_all_associations,
run_from_scratch, force):
### Test whether files already exist and if not downloads/builds them
if export_all_associations == 'no': ### Applies to EnsemblImport.py analyses
filename = 'AltDatabase/ucsc/' + species + '/' + species + '_UCSC_transcript_structure_mrna.txt'
else: ### Applies to the file used for Domain-level analyses
filename = 'AltDatabase/ucsc/' + species + '/' + species + '_UCSC_transcript_structure_COMPLETE-mrna.txt'
counts = verifyFile(filename, 'counts')
if counts < 9:
import UCSCImport
try:
UCSCImport.runUCSCEnsemblAssociations(species, mRNA_Type,
export_all_associations,
run_from_scratch, force)
except Exception:
UCSCImport.exportNullDatabases(
species) ### used for species not supported by UCSC
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
if __name__ == '__main__':
species = 'Hs'; #species_full = 'Drosophila_melanogaster'
filename = 'AltDatabase/ucsc/'+species+'/polyaDb.txt'
verifyFile(filename,species) ### Makes sure file is local and if not downloads.
sys.exit()
importEnsExonStructureData(species,[],[],[]);sys.exit()
reformatPolyAdenylationCoordinates(species,'no');sys.exit()
#test = 'yes'
#test_gene = ['ENSG00000140153','ENSG00000075413']
import UCSCImport; import update
knownAlt_dir = update.getFTPData('hgdownload.cse.ucsc.edu','/goldenPath/currentGenomes/'+species_full+'/database','knownAlt.txt.gz')
polyA_dir = update.getFTPData('hgdownload.cse.ucsc.edu','/goldenPath/currentGenomes/'+species_full+'/database','polyaDb.txt.gz')
output_dir = 'AltDatabase/ucsc/'+species + '/'
UCSCImport.downloadFiles(knownAlt_dir,output_dir); UCSCImport.downloadFiles(polyA_dir,output_dir);sys.exit()
ensembl_ucsc_splicing_annotations = importEnsExonStructureData(species,ensembl_gene_coordinates,ensembl_annotations,exon_annotation_db)
if __name__ == '__main__':
species = 'Hs'
#species_full = 'Drosophila_melanogaster'
filename = 'AltDatabase/ucsc/' + species + '/polyaDb.txt'
verifyFile(filename,
species) ### Makes sure file is local and if not downloads.
sys.exit()
importEnsExonStructureData(species, [], [], [])
sys.exit()
reformatPolyAdenylationCoordinates(species, 'no')
sys.exit()
#test = 'yes'
#test_gene = ['ENSG00000140153','ENSG00000075413']
import UCSCImport
import update
knownAlt_dir = update.getFTPData(
'hgdownload.cse.ucsc.edu',
'/goldenPath/currentGenomes/' + species_full + '/database',
'knownAlt.txt.gz')
polyA_dir = update.getFTPData(
'hgdownload.cse.ucsc.edu',
'/goldenPath/currentGenomes/' + species_full + '/database',
'polyaDb.txt.gz')
output_dir = 'AltDatabase/ucsc/' + species + '/'
UCSCImport.downloadFiles(knownAlt_dir, output_dir)
UCSCImport.downloadFiles(polyA_dir, output_dir)
sys.exit()
ensembl_ucsc_splicing_annotations = importEnsExonStructureData(
species, ensembl_gene_coordinates, ensembl_annotations,
exon_annotation_db)