def operate(cathcode,inputDirectory="/home/inab/databases/flat/pdb", workingDirectory="/home/inab/www/CATHdomain", host="okazaki.cnb.csic.es", user="******", passwd="R7xvgAKK", db="sflexfit", verbose=False):
cATHfamilyLoader = CATHfamilyLoader(cathcode, host, user, passwd, db, workingDirectory)
cATHfamilyLoader.getFamilyPDBS()
cATHfamilyLoader.INB_downloadPDBfiles(inputDirectory, verbose=verbose)
cATHfamilyLoader.INB_uncompressPDBFiles(inputDirectory, verbose=verbose)
cATHfamilyLoader.extractDomains(verbose=verbose)
compressedFileName = os.path.join(workingDirectory,cathcode)
cATHfamilyLoader.compressResults(compressedFileName)
logFileName = os.path.join(workingDirectory,cathcode+".log")
#cATHfamilyLoader.deleteAll(logFileName, verbose)
return os.path.join(workingDirectory,cathcode+".tgz")
def operate(cathcode, workingDirectory, host, user, passwd, db, verbose,tar,justTar):
if verbose:
print ("getting domains for %s superfamily"% (cathcode,))
cATHfamilyLoader = CATHfamilyLoader(cathcode, host, user, passwd, db, workingDirectory)
if verbose:
print "getting information from DB"
cATHfamilyLoader.getFamilyPDBS()
if verbose:
print "downloading pdb files"
cATHfamilyLoader.downloadPDBfiles(verbose=verbose)
if verbose:
print "uncompressing pdb files"
cATHfamilyLoader.uncompressPDBFiles(verbose=verbose)
if verbose:
print "extracting domains"
cATHfamilyLoader.extractDomains(verbose=verbose)
if verbose:
print "generating domain list for mmult"
cATHfamilyLoader.generateDomainList(verbose=verbose)
#
compressedFileName = path.join(workingDirectory,cathcode)
#
if tar:
cATHfamilyLoader.compressResults(compressedFileName)
logFileName = path.join(workingDirectory,cathcode+".log")
if justTar:
cATHfamilyLoader.deleteAll(logFileName, verbose=True)
if verbose:
print ("finished. You can find the resulting tgz at %s" % (path.join(workingDirectory,cathcode+".tgz"),))
else:
cATHfamilyLoader.deleteCompressedPDBS(verbose)
if verbose and not tar:
print ("finished. You can find the log file at %s" % (path.join(workingDirectory,cathcode+".log"),))