def clip_parmdb(sb):
run_process(
input_parset.getString("pdbclip.executable"),
"--auto",
"--sigma=%f" % (input_parset.getFloat("pdbclip.sigma"),),
os.path.join(sb, "instrument"),
)
def transfer_calibration(ms_pair):
cal, target = ms_pair
print "Transferring solution from %s to %s" % (cal, target)
parmdb_name = mkdtemp(dir=scratch)
run_process("parmexportcal", "in=%s/instrument/" % (cal, ),
"out=%s" % (parmdb_name, ))
run_process("calibrate-stand-alone", "--parmdb", parmdb_name, target,
transfer_parset, transfer_skymodel)
def run_blastn(query, db, out, threads, qcov=25, pid=98, evalue=1e-5):
cmd = "blastn "
cmd += "-query %s " % query
cmd += "-db %s " % db
cmd += "-out %s " % out
cmd += "-outfmt '6 std qlen slen' "
cmd += "-max_target_seqs 1 "
cmd += "-max_hsps 1 "
cmd += "-qcov_hsp_perc %s " % qcov
cmd += "-perc_identity %s " % pid
cmd += "-evalue %s " % evalue
cmd += "-num_threads %s " % threads
utility.run_process(cmd)
def run_mash(mash_sketch, fna_path, tmp_dir, threads=1):
out_path = '%s/mash.dist' % tmp_dir
command = "mash dist -p %s -d 0.25 %s %s > %s" % (threads, fna_path,
mash_sketch, out_path)
out, err = utility.run_process(command)
with open(tmp_dir + '/id_map.tsv', 'w') as f:
for id, rec in enumerate(utility.parse_mash(out_path)):
f.write(str(id) + '\t' + rec['target'] + '\n')
def blastn(query, target, outdir, id):
out_path = outdir + '/' + id + '.m8'
if not os.path.exists(out_path):
cmd = "blastn -outfmt '6 std qlen slen' "
cmd += "-max_target_seqs 1 -max_hsps 1 "
cmd += "-query %s -subject %s " % (query, target)
out, err = utility.run_process(cmd)
open(out_path, 'w').write(out)
else:
out = open(out_path).read()
return out
def clip_parmdb(sb):
run_process(input_parset.getString("pdbclip.executable"), "--auto",
"--sigma=%f" % (input_parset.getFloat("pdbclip.sigma"), ),
os.path.join(sb, "instrument"))
aw_parset_name,
target_info["skymodel"],
input_parset.getString("make_mask.executable"),
scratch,
awim_init=awim_init)
with time_code("Making images"):
for target_info in ms_target.values():
print "Making image %s" % target_info["output_im"]
print run_awimager(
aw_parset_name, {
"ms": target_info["bl_limit_ms"],
"mask": target_info["mask"],
"threshold": "%fJy" % (target_info["threshold"], ),
"image": target_info["output_im"],
"wmax": maxbl
},
initscript=awim_init)
print "Updaging metadata in %s" % target_info["output_im"]
run_process(
"addImagingInfo",
"%s.restored.corr" % target_info["output_im"],
"", # No sky model specified
"0",
str(maxbl),
target_info["output_ms"])
print "Saving mask for %s to %s" % (
target_info["output_im"], target_info["output_im"] + ".mask")
shutil.copytree(target_info["mask"],
target_info["output_im"] + ".mask")
def transfer_calibration(ms_pair):
cal, target = ms_pair
print "Transferring solution from %s to %s" % (cal, target)
parmdb_name = mkdtemp(dir=scratch)
run_process("parmexportcal", "in=%s/instrument/" % (cal,), "out=%s" % (parmdb_name,))
run_process("calibrate-stand-alone", "--parmdb", parmdb_name, target, transfer_parset, transfer_skymodel)
input_parset.getString("make_mask.executable"),
scratch,
awim_init=awim_init,
)
with time_code("Making images"):
for target_info in ms_target.values():
print "Making image %s" % target_info["output_im"]
print run_awimager(
aw_parset_name,
{
"ms": target_info["bl_limit_ms"],
"mask": target_info["mask"],
"threshold": "%fJy" % (target_info["threshold"],),
"image": target_info["output_im"],
"wmax": maxbl,
},
initscript=awim_init,
)
print "Updaging metadata in %s" % target_info["output_im"]
run_process(
"addImagingInfo",
"%s.restored.corr" % target_info["output_im"],
"", # No sky model specified
"0",
str(maxbl),
target_info["output_ms"],
)
print "Saving mask for %s to %s" % (target_info["output_im"], target_info["output_im"] + ".mask")
shutil.copytree(target_info["mask"], target_info["output_im"] + ".mask")