def _save_aln_results(self, save_dir=None):
'''
first parse the blast result file,
and then save alignment files into the save_dir.
if save_dir is not defined,
it does not perform any operations.
'''
if self.save_dir == None and save_dir == None:
return
elif save_dir == None:
save_dir = self.save_dir
blast = self.parse()
self.msas = {}
for i, msa in enumerate(blast):
iter = i + 1
dir, basename, ext = parse_sequence_filename(self.input)
profile_name = build_profile_filename(save_dir, basename, iter,
'.aln')
profile_fp = open(profile_name, 'w')
msa.build_psiblast_alignment_input(profile_fp)
profile_fp.close()
self.aln_files[iter] = profile_name
self.msas[iter] = msa
def __init__(self, input_file=None, output_file=None):
if input_file == None:
raise TypeError("No Input file is given.")
if output_file == None:
dir, base_filename, iteration, ext = parse_profile_filename(
input_file)
output_file = build_profile_filename(dir, base_filename, iteration,
".pnp")
self.input_file = input_file
self.output_file = output_file
def initial_iteration(self, echo=True):
'''
Run initial blast and prepare output
'''
#run blast
temp_output = os.path.join(
self.temp_dir, '%s.1%s' % (self.output_base, self.output_ext))
runner = BLASTRunner(input=self.processed_input,
output=temp_output,
**self.kwargs)
runner.run()
#parse blast output
blast = BLAST.BLAST(self.processed_input, runner.output)
msa = blast[-1]
#flagging for combining HSPs for B input alignment.
msa.set_combine_hsps()
#purge the result
if self.use_overlapping_purging:
if echo:
print('purging overlapping regions...')
#build pssm
#for initial iteration, BLOSUM 62 matrix is used!
pssm = ScoreMat() # len(self.processed_inputfasta) )
pssm.set_blosum_mat()
#start to purge the matrix
if self.number_of_processors > 1:
msa.purge_overlapping_hsps_multithreading(
self.inserted_positions, pssm, self.number_of_processors)
else:
msa.purge_overlapping_hsps(self.inserted_positions, pssm)
if self.use_backblast_purging:
for neighbor_msa in self.neighboring_msas:
#msa.psiblast_purge( neighbor_msa )
backblastpurger = BackblastPurger(msa, neighbor_msa,
**self.kwargs)
msa_output = build_profile_filename(self.temp_dir, self.output_base, 1,
'.aln')
msa_output_fp = open(msa_output, 'w')
msa.build_psiblast_alignment_input(msa_output_fp)
msa_output_fp.close()
self.current_runner = runner
self.current_msa_output = msa_output
self.current_iteration = 1
self.current_parser = blast
self.msa_files.append(msa_output)
return msa #msa
def __init__(self,
cmd=None,
input_file=None,
output_file=None,
calibration_db=None,
calibrate=True,
calibration_cmd=None):
if cmd == None:
cmd = Settings.get("hhmake")
if input_file == None:
raise TypeError("Input_file should be given.")
if calibration_cmd == None:
calibration_cmd = Settings.get("hhsearch_cmd")
if calibration_db == None:
calibration_db = Settings.get("hhm_cal_db")
if output_file == None:
dir, base_filename, iteration, ext = parse_profile_filename(
input_file)
output_file = build_profile_filename(dir, base_filename, iteration,
'.hhm')
self.cmd = cmd
self.calibration_cmd = calibration_cmd
self.calibration_db = calibration_db
self.calibrate = calibrate
self.input_file = input_file
self.output_file = output_file
#the following part is added due to hhsearch bug
#of cannot handle long input file name handling!
self.tmpinput = tempfile.NamedTemporaryFile()
self.tmpinputname = self.tmpinput.name
try:
shutil.copy(self.input_file, self.tmpinputname)
except IOError:
self.tmpinputname = self.input_file
self.tmpoutput = tempfile.NamedTemporaryFile()
self.tmpoutputname = self.tmpoutput.name
#need to be copied after the execution!
self.command_lines = self.get_command_lines()
def next_iteration(self, echo=True):
self.current_iteration += 1
self.previous_runner = self.current_runner
self.previous_msa_output = self.current_msa_output
self.previous_parser = self.current_parser
i = self.current_iteration
temp_output = os.path.join(
self.temp_dir,
'%s.%s%s' % (self.output_base, str(i), self.output_ext))
runner = BLASTRunner(input=self.processed_input,
output=temp_output,
input_alignment=self.previous_msa_output,
**self.kwargs)
runner.run()
blast = BLAST.BLAST(self.processed_input, runner.output)
msa = blast[-1]
msa.set_combine_hsps()
if self.use_overlapping_purging:
if echo:
print('purging overlapping regions...')
pssm = ScoreMat()
pssm.build_pssm(self.previous_parser[-1], **self.kwargs)
msa.purge_overlapping_hsps(self.inserted_positions, pssm)
if self.use_backblast_purging:
for neighbor_msa in self.neighboring_msas:
#msa.psiblast_purge( neighbor_msa )
backblastpurger = BackblastPurger(msa, neighbor_msa)
#make msa output
msa_output = build_profile_filename(self.temp_dir, self.output_base, i,
'.aln')
msa_output_fp = open(msa_output, 'w')
msa.build_psiblast_alignment_input(msa_output_fp)
msa_output_fp.close()
#finally
self.current_runner = runner
self.current_msa_output = msa_output
self.current_parser = blast
self.msa_files.append(msa_output)
return msa
def set_result_files( self ) :
'''
returns list of a3m files in the save_dir.
'''
basename = parse_profile_filename( self.sequence )[1]
if not basename :
return
a3m_files = glob.glob( os.path.join( self.save_dir, basename + '*.a3m' ) )
new_a3m_files = []
for a3m in a3m_files :
dir, basename2, iteration, ext = parse_profile_filename( a3m )
newa3m = build_profile_filename( dir, basename, iteration, ext )
shutil.move( a3m, newa3m )
new_a3m_files.append( newa3m )
self.a3m_files = new_a3m_files
self.a3m_files.sort()
def get_command_line(self):
if self.input_type == None:
self.input_type = 'a3m'
if self.output_type == None:
self.output_type = 'psi'
if self.output_file == None:
dir, base_filename, iteration, ext = parse_profile_filename(
self.input_file)
self.output_file = build_profile_filename(dir, base_filename,
iteration,
'.' + self.output_type)
command_line = [
self.cmd, self.input_type, self.output_type, self.input_file,
self.output_file
]
return command_line
def get_command_line(self):
if self.output_file == None:
dir, base_filename, iteration, ext = parse_profile_filename(
self.input_file)
if verbose:
print("COMPASS Builder file analysis")
print('input_file', self.input_file)
print("dir:", dir)
print("base_filename:", base_filename)
print("ieration:", iteration)
print("ext:", ext)
self.output_file = build_profile_filename(dir, base_filename,
iteration, '.cnp')
self.temporary_output_fp = tempfile.NamedTemporaryFile()
self.temporary_output_file = self.temporary_output_fp.name
list_fn = self.prepare_list_file()
command_line = [
self.cmd, '-i', list_fn, '-o', self.temporary_output_file
]
return command_line
def build_file(self, dominfo):
from evdblib.DBTools import Settings
filename = os.path.join(self.job_dir,
'prfs%s.job' % dominfo['uniqueid'])
if not self.cmd:
self.cmd = Settings.get('profile_searcher')
command = self.cmd
domain_path = dominfo['domain_path']
profile_search_method = self.alignment_method
profile_search_queryid = dominfo['uniqueid']
iteration = self.iteration
query_iteration = min(self.iteration, check_profile_integrity(dominfo))
profile_search_query = build_profile_filename(
domain_path, dominfo['uniqueid'] + '.prof', query_iteration,
self.profile_extention)
profile_search_db = self.search_db
profile_search_db_size = self.search_db_size
profile_search_output = build_sequence_filename(
domain_path, dominfo['uniqueid'], self.alignment_extention)
command += ' -q %(profile_search_queryid)s -j %(iteration)s -m %(profile_search_method)s -u -s %(profile_search_db_size)s -d %(profile_search_db)s %(profile_search_query)s %(profile_search_output)s' % locals(
)
if os.path.exists(filename):
raise JobScriptWriteError(
"Profile search job script %s already exists!" % filename)
fp = open(filename, 'w')
print(command, file=fp)
fp.close()
return filename
def _prepare_compass_search_db(db_filename, domain_informations, iteration,
use_between, selected_iterations):
'''
prepare compass DB.
'''
db_fp = open(db_filename, 'w')
ext = Settings.get('compass_suffix')
db_size_fp = open(db_filename + ".len", 'w') #need to be built
compass_db_size = 0
previous_iteration = selected_iterations[max(
selected_iterations.index(iteration) - 1, 0)]
number_of_records = 0
for dominfo in domain_informations:
#read domain path
domain_path = dominfo['domain_path']
if not domain_path:
if verbose:
print("WARNING: Dominfo does not have domain_path...")
print(dominfo)
continue
domid = dominfo['uniqueid']
compass_file = build_profile_filename(domain_path, domid + '.prof',
iteration, ext)
if not os.path.exists(compass_file) and use_between:
#in case the hhsearch file of the iteration
#does not exists
#and the use_between flag is On...
#find the last iteration
last_available_iteration = check_profile_integrity(dominfo)
if not last_available_iteration:
print("WARNING: Profile is bad!", domain_path, domid)
continue
if last_available_iteration > previous_iteration:
compass_file = build_profile_filename(
domain_path, domid + '.prof', last_available_iteration,
ext)
else:
if verbose:
print("No between iteration available!", iteration,
last_available_iteration)
continue
elif not os.path.exists(compass_file) and not use_between:
#when hhsearch file is not availble and use between flag is off.
last_available_iteration = check_profile_integrity(dominfo)
compass_file = build_profile_filename(domain_path, domid + '.prof',
last_available_iteration,
ext)
#final check!
if not os.path.exists(compass_file):
#error!
print("WARNING: COMPASS file should be available but not found!",
compass_file,
file=sys.stderr)
raise SearchDatabasePreparationError(
"COMPASS numerical profile file is not availble!",
compass_file)
continue
fp = open(compass_file)
content = fp.read()
fp.close()
db_fp.write(content)
number_of_records += 1
compass_size_file = compass_file + ".len"
try:
fp = open(compass_size_file)
compass_db_size += int(fp.read().strip())
fp.close()
except:
print("WARNING: Cannot read compass profile size file.",
compass_size_file)
db_fp.close()
print(compass_db_size, file=db_size_fp)
db_size_fp.close()
return number_of_records
def _prepare_hhsearch_search_db(db_filename, domain_informations, iteration,
use_between, selected_iterations):
'''
prepare HHsearch DB.
and returns the number of records saved in the database file.
'''
db_fp = open(db_filename, 'w')
ext = Settings.get('hhm_suffix')
#getting previous iteration
#for selecting iteration bigger than before.
previous_iteration = selected_iterations[max(
selected_iterations.index(iteration) - 1, 0)]
number_of_records = 0
for dominfo in domain_informations:
#read domain path
if 'domain_path' in dominfo:
domain_path = dominfo['domain_path']
else:
raise ValueError('domain_path does not exists', dominfo)
if not domain_path:
if verbose:
print("WARNING: Dominfo does not have domain_path...")
print(dominfo)
continue
domid = dominfo['uniqueid']
hhsearch_file = build_profile_filename(domain_path, domid + '.prof',
iteration, ext)
if not os.path.exists(hhsearch_file) and use_between:
#in case the hhsearch file of the iteration
#does not exists
#and the use_between flag is On...
#means the profile is generation is good!
#and the value is max iteratoin!!
last_available_iteration = check_profile_integrity(dominfo)
if not last_available_iteration:
print("WARNING: Profile is bad!", domain_path, domid)
continue
if last_available_iteration > previous_iteration:
hhsearch_file = build_profile_filename(
domain_path, domid + '.prof', last_available_iteration,
ext)
else:
if verbose:
print("WARNING: No between iteration available!",
iteration, last_available_iteration)
continue
elif not os.path.exists(hhsearch_file) and not use_between:
#when hhsearch file is not availble and use between flag is off.
last_available_iteration = check_profile_integrity(dominfo)
hhsearch_file = build_profile_filename(domain_path,
domid + '.prof',
last_available_iteration,
ext)
#final check!
if not os.path.exists(hhsearch_file):
#error!
print(
"Error: HHsearch HMM file should be available but not found!",
hhsearch_file,
file=sys.stderr)
raise SearchDatabasePreparationError(
"HHsearch HHM file is not availble!", hhsearch_file)
fp = open(hhsearch_file)
content = fp.read()
fp.close()
db_fp.write(content)
number_of_records += 1
db_fp.close()
return number_of_records