def main(args):
register_ctrl_c()
p = parse_args(args)
log_path = set_up_logging(p.debug, p.out)
log.info('python ' + __file__ + ' ' + ' '.join(args))
log.info('logging to ' + log_path)
log.info('')
try:
working_dir = p.out
with open(config.config_file) as f:
conf = dict(l.strip().lower().split('=', 1)
for l in f.readlines() if l.strip() and l.strip()[0] != '#')
check_and_install_tools(p.debug, conf.get('db_vendor', 'sqlite') == 'sqlite', log_path)
start_from, start_after = get_starting_step(p.start_from, join(p.out, log_fname))
log.debug('Changing to %s' % working_dir)
chdir(working_dir)
if not p.overwrite:
check_results_existence()
if not exists(config.intermediate_dir):
mkdir(config.intermediate_dir)
set_up_config(working_dir)
# Building the workflow
workflow = Workflow(working_dir, id=make_workflow_id(working_dir),
cmdline_args=['python', __file__] + args)
log.debug('Workflow id is "' + workflow.id + '"')
log.debug('')
suffix = '' if conf.get('db_vendor', 'sqlite') == 'sqlite' else '_' + workflow.id
njobs = p.threads or p.jobs or 30
workflow.extend([
step_prepare_proteomes_and_annotations(p),
steps.filter_proteomes(
min_length=int(p.min_length),
max_percent_stop=int(p.max_percent_stop)),
steps.make_blast_db(),
steps.blast(
workflow.id,
int(p.threads) or int(p.jobs) or 30,
on_cluster=njobs and not p.threads,
evalue=float(p.evalue)),
steps.parse_blast_results(),
steps.clean_database(suffix),
steps.install_schema(suffix),
steps.load_blast_results(suffix),
steps.find_pairs(suffix),
steps.dump_pairs_to_files(suffix),
steps.mcl(p.debug),
steps.step_save_orthogroups()])
result = workflow.run(
start_after, start_from,
overwrite=True,
ask_before=p.ask_each_step)
if result == 0:
log.info('Done.')
log.info('Log is in ' + join(working_dir, log_fname))
if isfile(join(working_dir, config.orthogroups_file)):
log.info('Groups are in ' + join(working_dir, config.orthogroups_file))
if isfile(config.nice_orthogroups_file):
log.info('Groups with aligned columns are in ' +
join(working_dir, config.nice_orthogroups_file))
else:
log.info('Groups in short format are in ' +
join(working_dir, config.short_orthogroups_file))
if isfile(log_fname):
with open(log_fname, 'a') as f:
f.write('\n')
return result
except (KeyboardInterrupt, SystemExit, GeneratorExit):
if isfile(log_fname):
with open(log_fname, 'a') as f:
f.write('\n')
return 1
except Exception as e:
log.error('')
log.exception('Unexpected error!')
if isfile(log_fname):
with open(log_fname, 'a') as f:
f.write('\n')
return 2
def main(args):
register_ctrl_c()
p = parse_args(args)
log_path = set_up_logging(p.debug, p.out)
log.info('python ' + __file__ + ' ' + ' '.join(args))
log.info('logging to ' + log_path)
log.info('')
try:
working_dir = p.out
with open(config.config_file) as f:
conf = dict(l.strip().lower().split('=', 1) for l in f.readlines()
if l.strip() and l.strip()[0] != '#')
check_and_install_tools(p.debug,
conf.get('db_vendor', 'sqlite') == 'sqlite',
log_path)
start_from, start_after = get_starting_step(p.start_from,
join(p.out, log_fname))
log.debug('Changing to %s' % working_dir)
chdir(working_dir)
if not p.overwrite:
check_results_existence()
if not exists(config.intermediate_dir):
mkdir(config.intermediate_dir)
set_up_config(working_dir)
# Building the workflow
workflow = Workflow(working_dir,
id=make_workflow_id(working_dir),
cmdline_args=['python', __file__] + args)
log.debug('Workflow id is "' + workflow.id + '"')
log.debug('')
suffix = '' if conf.get('db_vendor',
'sqlite') == 'sqlite' else '_' + workflow.id
njobs = p.threads or p.jobs or 30
workflow.extend([
step_prepare_proteomes_and_annotations(p),
steps.filter_proteomes(min_length=int(p.min_length),
max_percent_stop=int(p.max_percent_stop)),
steps.make_blast_db(),
steps.blast(workflow.id,
int(p.threads) or int(p.jobs) or 30,
on_cluster=njobs and not p.threads,
evalue=float(p.evalue)),
steps.parse_blast_results(),
steps.clean_database(suffix),
steps.install_schema(suffix),
steps.load_blast_results(suffix),
steps.find_pairs(suffix),
steps.dump_pairs_to_files(suffix),
steps.mcl(p.debug),
steps.step_save_orthogroups()
])
result = workflow.run(start_after,
start_from,
overwrite=True,
ask_before=p.ask_each_step)
if result == 0:
log.info('Done.')
log.info('Log is in ' + join(working_dir, log_fname))
if isfile(join(working_dir, config.orthogroups_file)):
log.info('Groups are in ' +
join(working_dir, config.orthogroups_file))
if isfile(config.nice_orthogroups_file):
log.info('Groups with aligned columns are in ' +
join(working_dir, config.nice_orthogroups_file))
else:
log.info('Groups in short format are in ' +
join(working_dir, config.short_orthogroups_file))
if isfile(log_fname):
with open(log_fname, 'a') as f:
f.write('\n')
return result
except (KeyboardInterrupt, SystemExit, GeneratorExit):
if isfile(log_fname):
with open(log_fname, 'a') as f:
f.write('\n')
return 1
except Exception as e:
log.error('')
log.exception('Unexpected error!')
if isfile(log_fname):
with open(log_fname, 'a') as f:
f.write('\n')
return 2
def main(args):
register_ctrl_c()
p = parse_args(args)
try:
if not exists(join(p.directory, 'intermediate')):
arg_parse_error('You need to run Scenario 1 on this directory first.')
if not p.out_dir:
p.out_dir = p.directory
working_dir = p.out_dir
with open(config_file) as cf:
conf = dict(
l.strip().split('=', 1) for l
in cf.readlines() if l.strip() and l.strip()[0] != '#')
start_from, start_after = get_starting_step(p.start_from, join(working_dir, log_fname))
if (not start_from or start_from == 1) and p.out_dir != p.directory:
log_text = ''
if isdir(p.out_dir):
if not p.overwrite:
files = [f for f in listdir(p.out_dir) if f and f[0] != '.']
#log.debug(files)
if files:
print('The output directory exists. Do you want to overwrite it? ' +
'(You can run with the --overwrite option to avoid this warning.)')
try:
raw_input('Press any key to overwrite and continue, or Ctrl+C to interrupt.\n> ')
except (EOFError, KeyboardInterrupt, SystemExit, GeneratorExit):
exit(1)
if exists(join(p.out_dir, log_fname)):
with open(join(p.out_dir, log_fname)) as log_f:
log_text = log_f.read()
rmtree(p.out_dir)
makedirs(p.out_dir)
rmdir(p.out_dir)
copytree(p.directory, p.out_dir)
if isfile(join(p.out_dir, log_fname)):
remove(join(p.out_dir, log_fname))
chdir(p.out_dir)
if log_text:
with open(join(p.out_dir, log_fname), 'w') as log_f:
log_f.write(log_text)
log_fpath = set_up_logging(p.debug, p.out_dir, 'a')
log.info('python ' + basename(__file__) + ' ' + ' '.join(args))
log.info('')
check_and_install_tools(p.debug, conf.get('db_vendor', 'sqlite'), log_fpath)
log.info('Changing to %s' % working_dir)
if not isdir(working_dir):
makedirs(working_dir)
chdir(working_dir)
set_up_config(working_dir)
# Building the workflow
workflow = Workflow(working_dir, id=make_workflow_id(working_dir),
cmdline_args=['python', __file__] + args)
log.info('Workflow id is "' + workflow.id + '"')
log.info('')
if conf.get('db_vendor', 'sqlite') == 'sqlite':
suffix = ''
else:
suffix = '_' + workflow.id
workflow.extend([
step_prepare_input(p),
steps.filter_proteomes(
min_length=int(p.min_length),
max_percent_stop=int(p.max_percent_stop)),
filter_new_proteomes(
new_proteomes_dir,
min_length=int(p.min_length),
max_percent_stop=int(p.max_percent_stop)),
steps.make_blast_db(),
steps.blast(
workflow.id,
p.threads or p.jobs or 30,
on_cluster=p.threads > 0,
new_good_proteomes=new_good_proteomes,
evalue=float(p.evalue)),
steps.parse_blast_results(),
steps.clean_database(suffix),
steps.install_schema(suffix),
steps.load_blast_results(suffix),
steps.find_pairs(suffix),
steps.dump_pairs_to_files(suffix),
steps.mcl(p.debug),
steps.step_save_orthogroups(new_proteomes_dir if not p.ids_list and p.blast_singletones else None)
])
blastdb = p.blastdb or conf.get('blastdb', None)
if not p.ids_list:
workflow.extend([step_blast_singletones(p.threads, p.blast_singletones, blastdb, p.debug, p.overwrite)])
result = workflow.run(
start_after, start_from,
overwrite=True,
ask_before=p.ask_each_step)
if result == 0:
log.info('Done.')
log.info('Log is in ' + join(working_dir, log_fname))
if isfile(join(working_dir, config.orthogroups_file)):
log.info('Groups are in ' + join(working_dir, config.orthogroups_file))
if isfile(config.nice_orthogroups_file):
log.info('Groups with aligned columns are in ' +
join(working_dir, config.nice_orthogroups_file))
else:
log.info('Groups in short format are in ' + join(working_dir, config.short_orthogroups_file))
return result
except (KeyboardInterrupt, SystemExit, GeneratorExit):
return 1
except Exception as e:
log.error('')
log.exception('Unexpected error!')
raise
parser.add_argument("-S", "--Storage",
help="Path to store data & results of the pipeline.",
type=str)
parser.add_argument("-P", "--ProjectName", nargs="?",
help="FICUS Study name Eg. hess/stegen/blanchard etc.",
type=str)
parser.add_argument("-I", "--Input",
help="\nA valid input\n"
"InputType: 1, An Integer\n"
"InputType: 2, A comma-seperated list of Integers\n"
"InputType: 3, A comma-seperated list of Integers\n",
type=str)
parser.add_argument("-C", "--CombineDatasets",
type=str2bool, nargs="?",
const=True, default=False,
help="Combine all dataset's MSGF & MASIC jobs to single file for generating crossTabs.")
parser.add_argument("-Sa", "--SelectAnalysis",
help="\n"
"internal : Run internal analysis\n"
"ficus : Run ficus analysis\n"
"both : Run both analysis\n",
type=str,
choices=["internal", "ficus", "both"])
return parser
if __name__ == '__main__':
args = return_argparser().parse_args()
start = Workflow(args.Mode, args.InputType, args.Storage ,args.ProjectName, args.Input, args.CombineDatasets, args.SelectAnalysis )
start.start_workflow()
def main(args):
register_ctrl_c()
p = parse_args(args)
try:
if not exists(join(p.directory, 'intermediate')):
arg_parse_error(
'You need to run Scenario 1 on this directory first.')
if not p.out_dir:
p.out_dir = p.directory
working_dir = p.out_dir
with open(config_file) as cf:
conf = dict(l.strip().split('=', 1) for l in cf.readlines()
if l.strip() and l.strip()[0] != '#')
start_from, start_after = get_starting_step(
p.start_from, join(working_dir, log_fname))
if (not start_from or start_from == 1) and p.out_dir != p.directory:
log_text = ''
if isdir(p.out_dir):
if not p.overwrite:
files = [
f for f in listdir(p.out_dir) if f and f[0] != '.'
]
#log.debug(files)
if files:
print(
'The output directory exists. Do you want to overwrite it? '
+
'(You can run with the --overwrite option to avoid this warning.)'
)
try:
raw_input(
'Press any key to overwrite and continue, or Ctrl+C to interrupt.\n> '
)
except (EOFError, KeyboardInterrupt, SystemExit,
GeneratorExit):
exit(1)
if exists(join(p.out_dir, log_fname)):
with open(join(p.out_dir, log_fname)) as log_f:
log_text = log_f.read()
rmtree(p.out_dir)
makedirs(p.out_dir)
rmdir(p.out_dir)
copytree(p.directory, p.out_dir)
if isfile(join(p.out_dir, log_fname)):
remove(join(p.out_dir, log_fname))
chdir(p.out_dir)
if log_text:
with open(join(p.out_dir, log_fname), 'w') as log_f:
log_f.write(log_text)
log_fpath = set_up_logging(p.debug, p.out_dir, 'a')
log.info('python ' + basename(__file__) + ' ' + ' '.join(args))
log.info('')
check_and_install_tools(p.debug, conf.get('db_vendor', 'sqlite'),
log_fpath)
log.info('Changing to %s' % working_dir)
if not isdir(working_dir):
makedirs(working_dir)
chdir(working_dir)
set_up_config(working_dir)
# Building the workflow
workflow = Workflow(working_dir,
id=make_workflow_id(working_dir),
cmdline_args=['python', __file__] + args)
log.info('Workflow id is "' + workflow.id + '"')
log.info('')
if conf.get('db_vendor', 'sqlite') == 'sqlite':
suffix = ''
else:
suffix = '_' + workflow.id
workflow.extend([
step_prepare_input(p),
steps.filter_proteomes(min_length=int(p.min_length),
max_percent_stop=int(p.max_percent_stop)),
filter_new_proteomes(new_proteomes_dir,
min_length=int(p.min_length),
max_percent_stop=int(p.max_percent_stop)),
steps.make_blast_db(),
steps.blast(workflow.id,
p.threads or p.jobs or 30,
on_cluster=p.threads > 0,
new_good_proteomes=new_good_proteomes,
evalue=float(p.evalue)),
steps.parse_blast_results(),
steps.clean_database(suffix),
steps.install_schema(suffix),
steps.load_blast_results(suffix),
steps.find_pairs(suffix),
steps.dump_pairs_to_files(suffix),
steps.mcl(p.debug),
steps.step_save_orthogroups(new_proteomes_dir if not p.ids_list
and p.blast_singletones else None)
])
blastdb = p.blastdb or conf.get('blastdb', None)
if not p.ids_list:
workflow.extend([
step_blast_singletones(p.threads, p.blast_singletones, blastdb,
p.debug, p.overwrite)
])
result = workflow.run(start_after,
start_from,
overwrite=True,
ask_before=p.ask_each_step)
if result == 0:
log.info('Done.')
log.info('Log is in ' + join(working_dir, log_fname))
if isfile(join(working_dir, config.orthogroups_file)):
log.info('Groups are in ' +
join(working_dir, config.orthogroups_file))
if isfile(config.nice_orthogroups_file):
log.info('Groups with aligned columns are in ' +
join(working_dir, config.nice_orthogroups_file))
else:
log.info('Groups in short format are in ' +
join(working_dir, config.short_orthogroups_file))
return result
except (KeyboardInterrupt, SystemExit, GeneratorExit):
return 1
except Exception as e:
log.error('')
log.exception('Unexpected error!')
raise