/usr/lib/python3/dist-packages/csb/apps/buildhmm.py is in python3-csb 1.2.3+dfsg-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Build an HMM from a FASTA sequence. This program is a proxy to hhblits/addss.pl
and hhmake from the HHpred package.
@note: assuming you have the full HHpred package installed and configured.
"""
import os
import abc
import csb.apps
import csb.core
import csb.io
from csb.bio.io.wwpdb import StructureParser
from csb.bio.io.hhpred import HHProfileParser
from csb.bio.io.fasta import FASTAOutputBuilder
from csb.bio.sequence import ChainSequence
class ExitCodes(csb.apps.ExitCodes):
IO_ERROR = 2
INVALID_DATA = 3
EXT_TOOL_FAILURE = 4
class AppRunner(csb.apps.AppRunner):
@property
def target(self):
return BuildProfileApp
def command_line(self):
cmd = csb.apps.ArgHandler(self.program, __doc__)
cmd.add_scalar_option('query-id', 'q', str, 'ID of the query, in PDB-like format (accessionCHAIN).'
'Used for naming the output files. Also, if the input is a PDB file with '
'multiple chains, CHAIN is used to pull the required chain from the file.',
required=True)
cmd.add_scalar_option('tk-root', 't', str, 'path to the ToolkitRoot folder in your HHsuite setup', default='/ebio/abt1_toolkit/share/wye')
cmd.add_scalar_option('database', 'd', str, 'custom HHblits database; if not defined, toolkit\'s unirpto20 will be used', default=None)
cmd.add_scalar_option('tk-config', 'c', str, 'path to a folder containing custom HHsuite configs (e.g. HHPaths.pm)', default='.')
cmd.add_scalar_option('cpu', None, int, 'maximum degree of parallelism', default=1)
cmd.add_boolean_option('no-ss', None, 'do not include secondary structure', default=False)
cmd.add_boolean_option('no-pseudo', None, 'do not add emission and transition pseudocounts', default=False)
cmd.add_boolean_option('no-calibration', None, 'do not calibrate the profile', default=False)
cmd.add_positional_argument('query', str, 'input sequence (FASTA or PDB file)')
return cmd
class BuildProfileApp(csb.apps.Application):
def main(self):
if os.path.isfile(self.args.query_id + '.hhm'):
BuildProfileApp.exit('# Profile "{0}" already exists, skipping'.format(self.args.query_id),
ExitCodes.CLEAN)
try:
self.log('# Building profile HMM for {0}...'.format(self.args.query))
pb = ProfileBuilder.create(self.args.query, self.args.query_id, self.args.database, self.args.tk_root, self.args.tk_config,
pseudo=not self.args.no_pseudo, ss=not self.args.no_ss, cpu=self.args.cpu)
pb.build_alignment()
pb.make_hmm()
if not self.args.no_calibration:
pb.calibrate_hmm()
except BuildArgError as ae:
BuildProfileApp.exit(str(ae), ExitCodes.INVALID_DATA)
except BuildIOError as ioe:
BuildProfileApp.exit(str(ioe), ExitCodes.IO_ERROR)
except csb.io.InvalidCommandError as ose:
msg = '{0!s}: {0.cmd}'.format(ose)
BuildProfileApp.exit(msg, ExitCodes.IO_ERROR)
except NoOutputError as noe:
msg = 'Expected file {0} not produced by: {1.cmd}.\nSTDERR: {1.stderr}\nSTDOUT: {1.stdout}'.format(noe.expected, noe.context)
BuildProfileApp.exit(msg, ExitCodes.EXT_TOOL_FAILURE)
except csb.io.ProcessError as pe:
msg = 'Bad exit code #{0.code} from: {0.cmd}.\nSTDERR: {0.stderr}\nSTDOUT: {0.stdout}'.format(pe.context)
BuildProfileApp.exit(msg, ExitCodes.EXT_TOOL_FAILURE)
self.log(' successfully created profile "{0}"'.format(self.args.query_id))
class BuildError(Exception):
pass
class BuildIOError(BuildError):
pass
class BuildArgError(BuildError):
pass
class NoOutputError(BuildError):
def __init__(self, expected, context, *args):
self.expected = expected
self.context = context
super(NoOutputError, self).__init__(*args)
class ProfileBuilder(object):
__metaclass__ = abc.ABCMeta
EMISSION_PSEUDO = '-pcm 4 -pca 2.5 -pcb 0.5 -pcc 1.0'
TRANSITION_PSEUDO = '-gapb 1.0 -gapd 0.15 -gape 1.0 -gapf 0.6 -gapg 0.6 -gapi 0.6'
@staticmethod
def create(query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1):
if database is None:
database = os.path.join(tk_root, "databases", "hhblits", "uniprot20")
if not os.path.isfile(query):
raise BuildIOError('File not found: ' + query)
for line in open(query):
if not line.strip():
continue
if line.startswith('>'):
return FASTAProfileBuilder(query, target_id, database, tk_root, tk_config, pseudo, ss, cpu)
elif line.startswith('HEADER') or line.startswith('ATOM'):
return PDBProfileBuilder(query, target_id, database, tk_root, tk_config, pseudo, ss, cpu)
else:
raise BuildArgError('Unknown input file format')
def __init__(self, query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1):
self.tk_root = tk_root
self.tk_config = tk_config
self.hhlib = os.path.join(tk_root, "bioprogs", "hhsuite")
if 'TK_ROOT' not in os.environ or not os.environ['TK_ROOT']:
os.putenv('TK_ROOT', self.tk_root)
if 'HHLIB' not in os.environ or not os.environ['HHLIB']:
os.putenv('HHLIB', self.hhlib)
os.environ["PATH"] += os.pathsep + os.path.join(self.hhlib, "bin")
self.query = query
self.accession = target_id[:-1]
self.chain = target_id[-1]
self.database = database
self.pseudo = bool(pseudo)
self.ss = bool(ss)
self.cpu = cpu
self._input = None
self._a3m = None
self._hhm = None
self.configure_input()
def run(self):
self.build_alignment()
self.make_hmm()
self.calibrate_hmm()
@property
def target_id(self):
return self.accession + self.chain
@abc.abstractmethod
def configure_input(self):
pass
def build_alignment(self):
assert self._input is not None
program = os.path.join(self.tk_root, 'bioprogs', 'hhsuite', 'bin', 'hhblits')
ali = self.target_id + '.a3m'
cmd = '{0} -cpu {1} -i {2} -d {3} -nodiff -oa3m {4}'.format(
program, self.cpu, self._input, self.database, ali)
bali = csb.io.Shell.run(cmd)
if bali.code != 0:
raise csb.io.ProcessError(bali)
if not os.path.isfile(ali):
raise NoOutputError(ali, bali)
if self.ss:
program2 = os.path.join(self.tk_root, 'bioprogs', 'hhsuite', 'scripts', 'addss.pl')
with csb.io.TempFile() as patch:
for l in open(program2):
if l.lstrip().startswith("use HHPaths"):
patch.write('use lib "{0}";\n'.format(self.tk_config))
patch.write(l);
patch.flush()
cmd2 = "perl {0} {1}".format(patch.name, ali)
addss = csb.io.Shell.run(cmd2)
if addss.code != 0:
raise csb.io.ProcessError(addss)
self._ali = ali
return ali
def make_hmm(self):
assert self._ali is not None
program = os.path.join(self.tk_root, 'bioprogs', 'hhpred', 'hhmake')
hhm = self.target_id + '.hhm'
cmd = '{0} -i {1} -o {2}'.format(program, self._ali, hhm)
if self.pseudo:
cmd = '{0} {1} {2}'.format(cmd, ProfileBuilder.EMISSION_PSEUDO, ProfileBuilder.TRANSITION_PSEUDO)
nnmake = csb.io.Shell.run(cmd)
if nnmake.code != 0:
raise csb.io.ProcessError(nnmake)
if not os.path.isfile(hhm):
raise NoOutputError(hhm, nnmake)
self._hhm = hhm
return hhm
def calibrate_hmm(self):
assert self._hhm is not None
program = os.path.join(self.tk_root, 'bioprogs', 'hhpred', 'hhsearch')
caldb = os.path.join(self.tk_root, 'databases', 'hhpred', 'cal.hhm')
cmd = '{0} -i {1}.hhm -d {2} -cal -cpu {3}'.format(program, self.target_id, caldb, self.cpu)
csb.io.Shell.runstrict(cmd)
class FASTAProfileBuilder(ProfileBuilder):
def configure_input(self):
if not os.path.isfile(self.query):
raise BuildIOError('File not found: ' + self.query)
fasta = self.target_id + '.fa'
with csb.io.EntryWriter(fasta) as f:
with open(self.query) as q:
f.write(q.read())
self._input = fasta
return fasta
class PDBProfileBuilder(ProfileBuilder):
def configure_input(self):
try:
s = StructureParser(self.query).parse()
chain = s.chains[self.chain]
except csb.core.ItemNotFoundError:
raise BuildArgError('Chain {0.chain} not found in {0.query}'.format(self))
except IOError as ioe:
raise BuildIOError(str(ioe))
fasta = self.target_id + '.fa'
with open(fasta, 'w') as f:
sequence = ChainSequence.create(chain)
FASTAOutputBuilder(f).add_sequence(sequence)
self._input = fasta
return fasta
def make_hmm(self):
super(PDBProfileBuilder, self).make_hmm()
self.format_structure()
def format_structure(self):
assert self._hhm is not None
pdb = self.target_id + '.pdb'
parser = HHProfileParser(self._hhm)
parser.format_structure(self.query, self.chain, pdb)
self._pdb = pdb
return pdb
def main():
AppRunner().run()
if __name__ == '__main__':
main()
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