wrap.add('wgs_insert_sd', [config['wgs_insert_sd']], create_dir=False)
wrap.add('wgs_base', [config['wgs_base']], create_dir=False)
# Variation
genomes = appconfig.find_files(config['community']['folder'], config['community']['seq'])
commPaths = [os.path.dirname(pn) for pn in genomes]
wrap.add('community', commPaths)
tableFolder = os.path.join(config['reference']['folder'], config['reference']['table_folder'])
tablePaths = appconfig.get_files(tableFolder, 'table')
wrap.add('comm_table', tablePaths, label_func=os.path.basename)
wrap.add('wgs_xfold', config['wgs_xfold'])
@wrap.add_target('run_quast')
@name_targets
def generate_wgs(outdir, c):
asm_path = os.path.join(config['wgs_folder'], '/'.join(outdir.split('/')[1:]), config['wgs_asmdir'])
ctg_file = '{0}/{1}.contigs.fasta'.format(asm_path, config['wgs_base'])
sources = ['{1[community][folder]}/{0[community]}/{0[refseq]}'.format(c, config), ctg_file]
target = os.path.join(outdir, 'quast/summary/report.html')
action = exec_env.resolve_action({
'sge': 'bin/sgerun_QUAST.sh $SOURCES.abspath $TARGET.abspath'.format(c, od=outdir)
})
return 'report', env.Command(target, sources, action)
wrap.add_controls(Environment())
def do_score(outdir, c):
cl_out = c['do_convert']['output']
ref_path = os.path.join(config['map_folder'], c['hic_path'])
ttable = appconfig.search_up(ref_path, config['truth_table'])
if ttable is None:
raise RuntimeError(
'Could not find an accompanying truth table for associated run {0}'
.format(c['hic_path']))
# this target consumes truth table and clustering output
source = [ttable, cl_out]
# this target creates 3 output files
target = [
'{0}.{1}'.format(cl_out, suffix) for suffix in ['f1', 'vm', 'bc']
]
action = exec_env.resolve_action({
'pbs':
'bin/pbsrun_SCORE.sh $SOURCES.abspath',
'sge':
'bin/sgerun_SCORE.sh $SOURCES.abspath',
'local':
'bin/all_scores.sh $SOURCES.abspath'
})
return env.Command(target, source, action)
wrap.add_controls(Environment())
