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")