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):
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)