def __init__(self, base, verbose):
self.base = base
self.to_convert = []
self.mainlog = set_verbosity.verbosity(__name__, verbose)
self.mainlog.debug('Creating new instance of Fetcher')
dir_funcs.makebase(base, self.mainlog)
return
def __init__(self, base, verbose):
self.base = base
self.to_convert = []
self.mainlog = set_verbosity.verbosity(__name__, verbose)
self.mainlog.debug('Creating new instance of Fetcher')
dir_funcs.makebase(base, self.mainlog)
return
def __init__(self, base, target, query, evalue, verbose):
"""Initialize the class with base directory, query sequence, e-value
threshold and verbosity level."""
self.query = query
self.evalue = float(evalue)
self.orthologues = {}
self.mainlog = set_verbosity.verbosity('BLAST_Search', verbose)
self.basedir = base
self.target = target
return
def __init__(self, base, target, query, evalue, verbose):
"""Initialize the class with base directory, query sequence, e-value
threshold and verbosity level."""
self.query = query
self.evalue = evalue
self.orthologues = {}
self.mainlog = set_verbosity.verbosity('BLAST_Search', verbose)
self.basedir = base
self.target = target
return
def __init__(self, base, deps, target, evalue, cfg, verbose):
self.mainlog = set_verbosity.verbosity('Setup_Env', verbose)
self.base = base
self.deps = deps
self.target_species = target
self.eval_thresh = str(evalue)
self.config_file = cfg
self.missing_progs = []
self.mainlog.debug('Config file in ' + self.config_file + '\n' +
'Setting variables: \n' + '#define BASE ' +
self.base + '\n' + '#define TARGET_SPECIES ' +
self.target_species + '\n' +
'#define EVAL_THRESHOLD ' + self.eval_thresh + '\n')
self.bash_path = spawn.find_executable('bash') or ''
self.gzip_path = spawn.find_executable('gzip') or ''
self.sum_path = spawn.find_executable('sum') or ''
self.tblastx_path = spawn.find_executable('tblastx') or ''
self.pasta_path = spawn.find_executable('run_pasta.py') or ''
self.hyphy_path = spawn.find_executable(
'HYPHYMP') or spawn.find_executable('hyphymp') or ''
self.clustalo_path = spawn.find_executable('clustalo') or ''
self.fasttree_path = spawn.find_executable('fasttree') or ''
self.mainlog.debug('Setting executable path variables:\n' +
'#define BASH ' + self.bash_path + '\n' +
'#define GZIP ' + self.gzip_path + '\n' +
'#define SUM ' + self.sum_path + '\n' +
'#define TBLASTX ' + self.tblastx_path + '\n' +
'#define PASTA ' + self.pasta_path + '\n' +
'#define HYPHY ' + self.hyphy_path + '\n' +
'#define CLUSTALO ' + self.clustalo_path + '\n' +
'#define FASTTREE ' + self.fasttree_path)
# Print out some warnings if executables are not found
if self.bash_path == '':
self.mainlog.error('Cannot find bash!')
if self.gzip_path == '':
self.mainlog.error('Cannot find gzip!')
if self.sum_path == '':
self.mainlog.error('Cannot find sum!')
if self.tblastx_path == '':
self.mainlog.warning('Cannot find tblastx!')
self.missing_progs.append('tBLASTx')
if self.pasta_path == '':
self.mainlog.warning('Cannot find PASTA!')
self.missing_progs.append('PASTA')
if self.hyphy_path == '':
self.mainlog.warning('Cannot find HyPhy!')
self.missing_progs.append('HyPhy')
if self.clustalo_path == '':
self.mainlog.warning('Cannot find Clustal-omega!')
self.missing_progs.append('ClustalO')
if self.fasttree_path == '':
self.mainlog.warning('Cannot find fasttree!')
self.missing_progs.append('fasttree')
return
def __init__(self, pasta_path, unaligned_sequences, query_sequence,
verbose):
self.mainlog = set_verbosity.verbosity('Pasta_Align', verbose)
# This is file-like object
self.input_seq = unaligned_sequences
# This will be populated with sequences for back-translation
self.input_dict = {}
self.query = query_sequence
self.pasta_path = check_modules.check_executable(pasta_path)
self.protein_input = None
self.aln_out = None
self.tree_out = None
self.final_aln = None
return
def __init__(self, base, deps, target, evalue, cfg, verbose):
self.mainlog = set_verbosity.verbosity('Setup_Env', verbose)
self.base = base
self.deps = deps
self.target_species = target
self.eval_thresh = str(evalue)
self.config_file = cfg
self.missing_progs = []
self.mainlog.debug(
'Config file in ' + self.config_file + '\n' +
'Setting variables: \n' +
'#define BASE ' + self.base + '\n' +
'#define TARGET_SPECIES ' + self.target_species + '\n' +
'#define EVAL_THRESHOLD ' + self.eval_thresh + '\n'
)
self.bash_path = spawn.find_executable('bash') or ''
self.gzip_path = spawn.find_executable('gzip') or ''
self.sum_path = spawn.find_executable('sum') or ''
self.tblastx_path = spawn.find_executable('tblastx') or ''
self.pasta_path = spawn.find_executable('run_pasta.py') or ''
self.hyphy_path = spawn.find_executable('HYPHYMP') or spawn.find_executable('hyphymp') or ''
self.mainlog.debug(
'Setting executable path variables:\n' +
'#define BASH ' + self.bash_path + '\n' +
'#define GZIP ' + self.gzip_path + '\n' +
'#define SUM ' + self.sum_path + '\n' +
'#define TBLASTX ' + self.tblastx_path + '\n' +
'#define PASTA ' + self.pasta_path + '\n' +
'#define HYPHY ' + self.hyphy_path)
# Print out some warnings if executables are not found
if self.bash_path == '':
self.mainlog.error('Cannot find bash!')
if self.gzip_path == '':
self.mainlog.error('Cannot find gzip!')
if self.sum_path == '':
self.mainlog.error('Cannot find sum!')
if self.tblastx_path == '':
self.mainlog.warning('Cannot find tblastx! Will download')
self.missing_progs.append('tBLASTx')
if self.pasta_path == '':
self.mainlog.warning('Cannot find PASTA! Will download')
self.missing_progs.append('PASTA')
if self.hyphy_path == '':
self.mainlog.warning('Cannot find HyPhy! Will download')
self.missing_progs.append('HyPhy')
return
def __init__(
self,
pasta_path,
unaligned_sequences,
query_sequence,
verbose):
self.mainlog = set_verbosity.verbosity('Pasta_Align', verbose)
# This is file-like object
self.input_seq = unaligned_sequences
# This will be populated with sequences for back-translation
self.input_dict = {}
self.query = query_sequence
self.pasta_path = check_modules.check_executable(pasta_path)
self.protein_input = None
self.aln_out = None
self.tree_out = None
self.final_aln = None
return
def main():
"""The main function."""
# The very first thing we do is do a base check to make sure that we can
# parse arguments
dep = check_modules.check_modules()
if dep:
check_modules.missing_mods(dep)
exit(1)
# Parse the arguments
# First, a check to see if any arguments were sent at all
# If not, then print the usage and exit
if not sys.argv[1:]:
parse_args.usage()
exit(1)
# Import the config handling script
import lrt_predict.Setup.parse_config as config
# vars() will convert from the weird Namespace type to a dictionary
arguments = vars(parse_args.parse_args())
# Pull out the verbosity switch right away
loglevel = set_verbosity.verbosity('LRT_Predict', arguments['loglevel'])
# If the config variable was passed
if 'config' in arguments:
# We ask then if the setup command was not passed
# If the user wants to setup, then don't bother trying to validate
# the config.
if arguments['action'] != 'setup':
cfg = config.ConfigHandler(
arguments['config'],
arguments,
arguments['loglevel'])
if cfg.is_valid():
cfg.read_vars()
config_opts = cfg.merge_options()
else:
loglevel.error('Config file is not valid!')
exit(1)
# Else, just set it to the options that were passed
else:
config_opts = arguments
else:
config_opts = arguments
arguments_valid, msg = parse_args.validate_args(config_opts, loglevel)
# If we got a return value that isn't False, then our arguments are good
if arguments_valid:
loglevel.debug(arguments_valid['action'] + ' subcommand was invoked')
# Which command was invoked?
if arguments_valid['action'] == 'setup':
setup(arguments_valid)
elif arguments_valid['action'] == 'fetch':
fetch(arguments_valid, loglevel)
elif arguments_valid['action'] == 'align':
# We will return the filename that contains the unaligned
# sequences, as we will use these as inputs for pasta
unaligned_seqs = blast(arguments_valid, loglevel)
# Then add the query sequence and align them
align(
arguments_valid,
unaligned_seqs,
loglevel)
elif arguments_valid['action'] == 'predict':
out = predict(arguments_valid, loglevel)
# copy the output file into the destination directory
# To build the output filename, we join the output directory
# with a new name based on the input filename
out_fname = os.path.join(
arguments_valid['output'],
os.path.basename(
arguments_valid['fasta'].replace(
'.fasta',
'_Predictions.txt')
)
)
open(out_fname, 'w').close()
shutil.copy2(out.name, out_fname)
loglevel.info('Prediction in ' + out_fname)
elif arguments_valid['action'] == 'compile':
compile_preds(arguments_valid, loglevel)
return
else:
loglevel.error(msg)
return
def main():
"""The main function."""
# The very first thing we do is do a base check to make sure that we can
# parse arguments
dep = check_modules.check_modules()
if dep:
check_modules.missing_mods(dep)
exit(1)
# Parse the arguments
# First, a check to see if any arguments were sent at all
# If not, then print the usage and exit
if not sys.argv[1:]:
parse_args.usage()
exit(1)
# Import the config handling script
import lrt_predict.Setup.parse_config as config
# vars() will convert from the weird Namespace type to a dictionary
arguments = vars(parse_args.parse_args())
# Pull out the verbosity switch right away
loglevel = set_verbosity.verbosity('LRT_Predict', arguments['loglevel'])
# If the config variable was passed
if 'config' in arguments:
# We ask then if the setup command was not passed
# If the user wants to setup, then don't bother trying to validate
# the config.
if arguments['action'] != 'setup':
cfg = config.ConfigHandler(arguments['config'], arguments,
arguments['loglevel'])
if cfg.is_valid():
cfg.read_vars()
config_opts = cfg.merge_options()
else:
loglevel.error('Config file is not valid!')
exit(1)
# Else, just set it to the options that were passed
else:
config_opts = arguments
else:
config_opts = arguments
arguments_valid, msg = parse_args.validate_args(config_opts, loglevel)
# If we got a return value that isn't False, then our arguments are good
if arguments_valid:
loglevel.debug(arguments_valid['action'] + ' subcommand was invoked')
# Which command was invoked?
if arguments_valid['action'] == 'setup':
setup(arguments_valid)
elif arguments_valid['action'] == 'fetch':
fetch(arguments_valid, loglevel)
elif arguments_valid['action'] == 'align':
# We will return the filename that contains the unaligned
# sequences, as we will use these as inputs for pasta
unaligned_seqs = blast(arguments_valid, loglevel)
# Then add the query sequence and align them
align(arguments_valid, unaligned_seqs, loglevel)
elif arguments_valid['action'] == 'predict':
out = predict(arguments_valid, loglevel)
# copy the output file into the destination directory
# To build the output filename, we join the output directory
# with a new name based on the input filename
out_fname = os.path.join(
arguments_valid['output'],
os.path.basename(arguments_valid['fasta'].replace(
'.fasta', '_Predictions.txt')))
open(out_fname, 'w').close()
shutil.copy2(out.name, out_fname)
loglevel.info('Prediction in ' + out_fname)
elif arguments_valid['action'] == 'compile':
compile_preds(arguments_valid, loglevel)
return
else:
loglevel.error(msg)
return
def __init__(self, outdir, verbose):
self.preddir = outdir
self.mainlog = set_verbosity.verbosity('HyPhy_Parser', verbose)
return
def __init__(self, outdir, verbose):
self.preddir = outdir
self.mainlog = set_verbosity.verbosity('HyPhy_Parser', verbose)
return