def make_wgs2ctg(outdir, c): com = c['community'] tbl = os.path.basename(c['comm_table']) # TODO find a better way to obtain the path to WGS reads query = appconfig.get_wgs_reads( os.path.join(os.path.abspath(config['wgs_folder']), com, tbl, str(c['wgs_xfold'])), config) # TODO likewise subject = os.path.join(os.path.abspath(config['wgs_folder']), com, tbl, str(c['wgs_xfold']), config['wgs_asmdir'], '{0[wgs_base]}.contigs.fasta'.format(config)) target = os.path.join(outdir, config['wgs2ctg']) source = [subject] + query action = exec_env.resolve_action({ 'pbs': 'bin/pbsrun_MAP.sh $SOURCES.abspath $TARGET.abspath', 'sge': 'bin/sgerun_MAP.sh $SOURCES.abspath $TARGET.abspath' }) return 'output', env.Command(target, source, action)
def generate_wgs(outdir, c): src_dir = os.path.join(config['wgs_folder'], '/'.join(outdir.split('/')[1:])) sources = ['{1}/{2}/{0[wgs_base]}.contigs.fasta'.format(c, src_dir, config['wgs_asmdir'])] + \ appconfig.get_wgs_reads(src_dir, config) target = os.path.join(outdir, 'lap_ctg.prob') action = exec_env.resolve_action({ 'pbs': 'bin/pbsrun_LAP.sh $SOURCES.abspath $TARGET.abspath'.format(c, od=outdir), 'sge': 'bin/sgerun_LAP.sh $SOURCES.abspath $TARGET.abspath'.format(c, od=outdir) }) return 'lap_ctg', env.Command(target, sources, action)
def generate_wgs(outdir, c): src_dir = os.path.join(config['wgs_folder'], '/'.join(outdir.split('/')[1:])) sources = ['{1[community][folder]}/{0[community]}/{0[refseq]}'.format(c, config)] + \ appconfig.get_wgs_reads(src_dir, config) target = os.path.join(outdir, 'lap_ref.prob') action = exec_env.resolve_action({ 'pbs': 'bin/pbsrun_LAP.sh $SOURCES.abspath $TARGET.abspath'.format(c, od=outdir), 'sge': 'bin/sgerun_LAP.sh $SOURCES.abspath $TARGET.abspath'.format(c, od=outdir) }) return 'lap_ref', env.Command(target, sources, action)
def generate_wgs(outdir, c): target = appconfig.get_wgs_reads(outdir, config) source = '{1[community][folder]}/{0[community]}/{0[refseq]}'.format(c, config) action = 'bin/sgerun_METAART.sh {0[seed]} {0[wgs_insert_length]} {0[wgs_insert_sd]} ' \ '{0[wgs_read_length]} {0[wgs_xfold]} {0[comm_table]} $SOURCE.abspath {0[wgs_base]} {od}'.format(c, od=outdir) return 'r1', 'r2', env.Command(target, source, action)