def __init__(self, database, search_type = 'prot'):
#Search Type Check
if search_type not in set(['prot','nucl']):
raise BE(-10)
self._search_type = search_type
#Blast executable configuration
self._configurator = ConfigParser.RawConfigParser(allow_no_value=True)
self._configurator.read(os.getenv('SBI_CONFIG_FILE',default_configuration_file))
self._exe = Executable(executable = self._configurator.get('blast','executable'),
path = self._configurator.get('blast','path'),
variable_path = self._configurator.get('blast','variable_path'))
#Database Configuration
self._database = self._check_database(os.path.abspath(database))
if os.path.isfile(self._database.file.full + ".idx"):
self._idx = File(file_name = self._database.file.full + ".idx", action = 'r')
else:
self._idx = None
#Adding fixed blast parameters
self._exe.add_attribute(self._database.file.full, '-db')
self._exe.add_attribute('5', '-outfmt')
self._exe.add_parameter('-lcase_masking')
SBIglobals.alert('debug', self, 'New Blast Executable created.\nBlast executable at {0}\n'.format(self._exe.full_executable))
self._selfHit = False
self._hitIDformat = 'single'
self._overwritte = False
self._clean_files = True
def __init__(self, fasta, threshold, output_dir=None, execute=True):
fasta = os.path.abspath(fasta)
if output_dir is None:
output_dir = os.path.split(fasta)[0]
if threshold >= 0.7: word = 5
elif threshold >= 0.6: word = 4
elif threshold >= 0.5: word = 3
elif threshold >= 0.4: word = 2
else: word = 1
#CDhit executable configuration
self._configurator = ConfigParser.RawConfigParser(allow_no_value=True)
self._configurator.read(
os.getenv('SBI_CONFIG_FILE', default_configuration_file))
self._exe = Executable(executable=self._configurator.get(
'cd-hit', 'executable'),
path=self._configurator.get('cd-hit', 'path'))
self._input = fasta
output_file = os.path.split(fasta)[1] + '.' + str(threshold).replace(
'.', '_')
self._output = os.path.join(output_dir, output_file)
self._threshold = str(threshold)
self._word = word
if execute:
self._execute()
def _check_database(self, database):
#Database file does not exist
if not os.path.isfile(database):
raise BE(code = -5, value = database)
#Database is not formated (if dbformatexe is added in the configuration path it will be autoformated)
formatdb_files = []
if self._search_type == 'nucl': formatdb_sufix = ['.nhr','.nin','.nsq']
elif self._search_type == 'prot': formatdb_sufix = ['.phr','.pin','.psq']
for sufix in formatdb_sufix:
if not os.path.isfile(database + sufix):
formatdb_files.append(database + sufix)
if len(formatdb_files) > 0:
try:
dbexe = Executable(executable = self._configurator.get('blast','dbformatexe'),
path = self._configurator.get('blast','path'),
variable_path = self._configurator.get('blast','variable_path'))
SBIglobals.alert('debug', self, 'Trying to format de DB {0} to perform a blast search.\n'.format(database))
dbexe.add_attribute(database, '-in')
dbexe.add_attribute(self._search_type, '-dbtype')
SBIglobals.alert('debug', self, 'Executing command {0}\n'.format(dbexe))
dbexe.execute()
except ConfigParser.NoOptionError, e:
raise BE(code = -6, value = formatdb_files)
except SystemError, e:
raise BE(code = -11, value = e)
def __init__(self, pdbfile, dsspfile, cleanpdb=False, cleandssp=False):
self._pdbfile = pdbfile
self._dsspfile = dsspfile
self._dsspdata = []
self._gapped = False
if DSSPExe._exe is None:
DSSPExe._exe = Executable(executable=DSSPExe._config.get(
'dssp', 'executable'),
path=DSSPExe._config.get('dssp', 'path'))
self._execute()
self._parse()
self._clean(cleanpdb, cleandssp)
class CDhitExe(object):
def __init__(self, fasta, threshold, output_dir=None, execute=True):
fasta = os.path.abspath(fasta)
if output_dir is None:
output_dir = os.path.split(fasta)[0]
if threshold >= 0.7: word = 5
elif threshold >= 0.6: word = 4
elif threshold >= 0.5: word = 3
elif threshold >= 0.4: word = 2
else: word = 1
#CDhit executable configuration
self._configurator = ConfigParser.RawConfigParser(allow_no_value=True)
self._configurator.read(
os.getenv('SBI_CONFIG_FILE', default_configuration_file))
self._exe = Executable(executable=self._configurator.get(
'cd-hit', 'executable'),
path=self._configurator.get('cd-hit', 'path'))
self._input = fasta
output_file = os.path.split(fasta)[1] + '.' + str(threshold).replace(
'.', '_')
self._output = os.path.join(output_dir, output_file)
self._threshold = str(threshold)
self._word = word
if execute:
self._execute()
@property
def output_file(self):
return self._output + '.clstr'
def _execute(self):
self._exe.add_attribute(self._input, '-i')
self._exe.add_attribute(self._output, '-o')
self._exe.add_attribute(self._threshold, '-c')
self._exe.add_attribute('1', '-g')
self._exe.add_attribute(self._word, '-n')
try:
self._exe.execute(silent=True)
except SystemError, e:
sys.stderr.write(
'Some error occurred while executing cd-hit\n{0}\n'.format(e))
def dynamic(executable, path):
DSSPExe._exe = Executable(executable=executable, path=path)
class BlastExe(object):
def __init__(self, database, search_type = 'prot'):
#Search Type Check
if search_type not in set(['prot','nucl']):
raise BE(-10)
self._search_type = search_type
#Blast executable configuration
self._configurator = ConfigParser.RawConfigParser(allow_no_value=True)
self._configurator.read(os.getenv('SBI_CONFIG_FILE',default_configuration_file))
self._exe = Executable(executable = self._configurator.get('blast','executable'),
path = self._configurator.get('blast','path'),
variable_path = self._configurator.get('blast','variable_path'))
#Database Configuration
self._database = self._check_database(os.path.abspath(database))
if os.path.isfile(self._database.file.full + ".idx"):
self._idx = File(file_name = self._database.file.full + ".idx", action = 'r')
else:
self._idx = None
#Adding fixed blast parameters
self._exe.add_attribute(self._database.file.full, '-db')
self._exe.add_attribute('5', '-outfmt')
self._exe.add_parameter('-lcase_masking')
SBIglobals.alert('debug', self, 'New Blast Executable created.\nBlast executable at {0}\n'.format(self._exe.full_executable))
self._selfHit = False
self._hitIDformat = 'single'
self._overwritte = False
self._clean_files = True
'''ATTRIBUTES'''
@property
def database(self): return self._database
@property
def selfHit(self): return self._selfHit
@selfHit.setter
def selfHit(self, vaule): self._selfHit = value
@property
def hitIDformat(self): return self._hitIDformat
@hitIDformat.setter
def hitIDformat(self, value):
if value not in set(['single','double','all']):
self._hitIDformat = 'single'
else:
self._hitIDformat = value
@property
def overwritte(self): return self._overwritte
@overwritte.setter
def overwritte(self, value): self._overwritte = value
@property
def clean_files(self): return self._clean_files
@clean_files.setter
def clean_files(self, value): self._clean_files = value
'''FUNCTIONS'''
def add_attribute(self, attribute_value, attribute_id):
if attribute_id in set(['-db','-outfmt']):
raise AttributeError('The parameters in {0} cannot be altered'.format(set(['-db','-outfmt'])))
self._exe.add_attribute(str(attribute_value), attribute_id)
def execute_query_seq(self, sequenceID = None, sequence = None, blast_input_file = None, blast_output_file = None):
if sequenceID is None and sequence is None:
raise AttributeError('Either a sequence or ID is needed to perform the blast')
if isinstance(sequenceID, (list,set,tuple)):
raise AttributeError('Blasts can only be executed one at a time due to XML output restrictions')
if sequenceID is None:
sequenceID = 'QuerySequence'
#Given only a code implies that the protein of interest is in the database itself
if sequence is None:
grabbedSequence = self._database.retrieve(sequenceID)
sequenceID = grabbedSequence.id
sequence = grabbedSequence.sequence
if len(re.sub(r'[Xx]','',sequence)) == 0: #All the sequence is unknown, it will crash blast
return BR.BlastResult(queryname=sequenceID, querylength=len(sequence))
file_prefixes = ".".join([str(os.getpid()), str(int(time.clock()*100000))])
if blast_input_file is None:
temp_input_name = os.path.join(os.getcwd(), file_prefixes + ".tmp.fa")
else:
temp_input_name = blast_input_file
if blast_output_file is None:
temp_output_name = os.path.join(os.getcwd(), file_prefixes + ".blast.xml.out")
else:
temp_output_name = blast_output_file
QueryFasta = Fasta.build(file_name = temp_input_name, sequenceID = sequenceID, sequence = sequence, force = True)
self._execute(input_file = QueryFasta, output_file = temp_output_name)
BlastResult = self._parse_blast(sequence, temp_output_name)
if self.clean_files:
self._clean([temp_input_name,temp_output_name])
return BlastResult
def execute_query(self, query_file = None, blast_output_file = None):
if isinstance(query_file, basestring) or isinstance(query_file, File):
newFasta = Fasta(fasta_file = query_file)
elif isinstance(query_file, Fasta):
newFasta = query_file
if newFasta.is_multifasta:
raise BE(code = -4, value = newFasta.file.full)
newFasta.load()
if len(re.sub(r'[Xx]','',newFasta.sequences[0].sequence)) == 0: #All the sequence is unknown, it will crash blast
return BR.BlastResult(queryname=newFasta.sequences[0].id, querylength=len(newFasta.sequences[0].sequence))
if blast_output_file is None:
temp_output_name = os.path.join(os.getcwd(), newFasta.file.prefix + "." + str(os.getpid()) + ".blast.xml.out")
else:
temp_output_name = blast_output_file
self._execute(input_file = newFasta, output_file = temp_output_name)
BlastResult = self._parse_blast(newFasta.sequences[0].sequence, temp_output_name)
if self.clean_files:
self._clean([temp_output_name])
return BlastResult
'''PRIVATE FUNCTIONS'''
def _execute(self, input_file, output_file):
if not os.path.isfile(output_file) or self.overwritte:
final_executable = copy.deepcopy(self._exe)
final_executable.add_attribute(input_file.file.full, '-query')
final_executable.add_attribute(output_file, '-out')
try:
final_executable.execute()
except SystemError, e:
psiblast_default_warning = 'Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported with PSSMs, resetting to default value of standard composition-based statistics'
selenocysteine_warning = 'Selenocysteine \(U\) at position'
if not bool(re.search(psiblast_default_warning,str(e))) and not bool(re.search(selenocysteine_warning,str(e))):
raise BE(code = -1, value = str(e))