def alnDict2output(aln_dict, dn, order='sorting'):
info = []
if len(aln_dict) == 0:
cmn.run('touch %s' % dn)
return None
#maxLength = max([len(each) for each in aln_dict.keys()])
maxLength = 0
maxNameLength = max([len(each) for each in aln_dict])
nameformat = '{:<%s}' % maxNameLength
names = list(aln_dict.keys())
if order == 'sorting':
names = sorted(names, key=lambda x: number4sorting(aln_dict[x]))
elif order == 'grouping':
#this is used to output inconsistent group
#rank by grouping of species IDs
names = sorted(names, key=lambda x: group_by_spnames(x))
else:
names.sort()
for i, name in enumerate(names):
#name = 'readgroup%s' % i
aln = aln_dict[name]
name = nameformat.format(name)
toAdd = maxLength - len(aln)
if toAdd > 0:
aln += '-' * toAdd
info.append('%s %s\n' % (name, ''.join(aln)))
cmn.write_file(''.join(info), dn)
def old_log_newBaits_ifPossible(seqs):
fall = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/species_barcodes_4mapping.fa'
takenNames = set(
[each.strip()[1:] for each in cmn.cmd2lines('grep ">" %s' % fall)])
fnew = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/addedBaits_fromPipeline.fa'
seqDict = read_fa(fnew)
for name in seqs:
if name not in takenNames and (name not in seqDict):
seqDict[name] = seqs[name][20:678]
with open(fnew, 'w') as dp:
for name in seqDict:
if name not in takenNames and (name not in seqDict):
print('saving %s into database...' % name)
fasta = '>%s\n%s\n' % (name, seqDict[name])
dp.write(fasta)
fverify = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/all_barcodes_4verify.fa'
dict2 = read_fa(fverify)
seqDict.update(dict2)
with open(fverify, 'w') as dp:
for name in seqDict:
fasta = '>%s\n%s\n' % (name.replace(
'(assembled)', '').strip('.'), seqDict[name].replace('-', 'N'))
dp.write(fasta)
cmd = 'module add blast;cd /project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes; makeblastdb -in=all_barcodes_4verify.fa -dbtype=nucl; chmod a+w all_barcodes_4verify.*'
cmn.run(cmd)
def parse_IDmapping_and_newDict(fn):
print('processing fasta names...')
cmd = 'source /home2/wli/.bash_profile; rename_fa_fullname.py %s > tmp.namelog' % fn
cmn.run(cmd)
seqDict = read_fa(fn + '.renamed')
IDmapping = names2IDs(list(seqDict.keys()))
return IDmapping, seqDict
def compute_mash_distance(f1, f2):
global cpu
dn = '/tmp/%s-%s' % (cmn.lastName(f1), cmn.lastName(f2))
cmd = '/home2/wli/local/mash-Linux64-v1.1.1/mash dist -p %s %s %s > %s' % (
cpu, f1, f2, dn)
cmn.run(cmd)
#print 'cmd:', cmd
dist = cmn.txt_read(dn).strip().split()[2]
return dist
def makeBlastDatabase(seqDict):
dn = 'db4picking.fa'
new = ['>%s\n%s\n' % (name, seqDict[name])
for name in seqDict
if seqDict[name].strip('N-X') != '']
cmn.write_file(''.join(new), dn)
cmd = 'module add blast; makeblastdb -dbtype=nucl -in=%s' % dn
cmn.run(cmd)
return dn
def transfer_alea_files(fnlist):
global transferDir
newlist = []
for fn in fnlist:
print('transfering %s from archive server ...' % fn)
cmd = 'rsync -r [email protected]:%s %s' % (fn, transferDir)
cmn.run(cmd)
newlist.append('%s/%s' % (transferDir, cmn.lastName(fn)))
return newlist
def separate_by_pair(fastqs, wdir):
print(wdir)
pdict = {}
mapdict = {}
for fastq in fastqs:
key = '.'.join(cmn.lastName(fastq).split('.')[:-1])
mapdict[key] = fastq
names = list(mapdict.keys())
length = max([len(name) for name in names])
for i in range(length):
if len(names) == 0:
break
checks = [name[:-1 - i] for name in names]
count_dict = Counter(checks)
for key in count_dict:
if count_dict[key] == 2: # got paired
paired_names = [each for each in names if each.startswith(key)]
fns = [mapdict[name] for name in paired_names]
pdict[key] = fns
#remove it from the list
for name in paired_names:
names.remove(name)
if len(pdict) == 0:
print('Error! fastq lib name not recognized, contact Wenlin for help!')
sys.exit()
singleLibs = [mapdict[name] for name in names]
print(singleLibs)
if len(singleLibs) > 1:
print(
'Warnning: more than one lib detected as single lib. below is the single list:'
)
print('\n'.join(singleLibs))
print('Email Wenlin for help')
#print 'paired libs are:'
#for key in pdict:
# print pdict[key]
#print '\nsingle libs are:'
#print ' '.join(singleLibs)
singleFn = '%s/single.fq' % wdir
if cmn.filexist(singleFn):
cmn.run('rm %s' % singleFn)
for fn in singleLibs:
cmn.run('cat %s/%s >> %s' % (wdir, fn, singleFn))
return pdict, singleFn
def update_baits(bait_dict):
adict = {}
for i, name in enumerate(bait_dict):
fnlabel = 'bait%s' % i
dn = 'baits/%s.fa' % fnlabel
seq = bait_dict[name]
fasta = '>%s\n%s\n' % (name, ''.join(seq))
cmn.write_file(fasta, dn)
cmd = 'module add bwa; bwa index %s -p %s' % (dn, fnlabel)
cmn.run(cmd)
adict[name] = dn
return adict
def read_refN(ref_genomes):
adict = {}
for ref in ref_genomes:
fN = '%s/%s_scaf_header.lines' % (ref_dir, ref)
#print fN
if not cmn.filexist(fN):
fhead = '%s/%s_scaf.header' % (ref_dir, ref)
cmd = 'wc -l %s > %s' % (fhead, fN)
cmn.run(cmd)
N = int(cmn.txt_read(fN).split()[0])
adict[ref] = N
return adict
def backup_finalStat(wdir):
ddir = '/project/biophysics/Nick_lab/mtang/archive/step4_postprocessing/final_stats/'
fns = cmn.cmd2lines('ls %s/*.report| grep -v all_genome' % wdir)
for fn in fns:
print('processing %s...' % fn)
fnlabel = cmn.lastName(fn)
#don't back up the ones without species
items = fnlabel.replace('_stat.report', '').split('_')
if len(items) == 1:
print('skip the fasta without sp for %s' % fn)
continue
#get the one with least NA and more data amount
dn = '%s/%s' % (ddir, fnlabel)
if os.path.exists(dn):
print('merging new and old data for %s' % fnlabel)
Nold_na, Nold_data = count_final_stat(dn)
Nnew_na, Nnew_data = count_final_stat(fn)
if Nnew_na < Nold_na: #less NA
cmn.run('cp %s %s' % (fn, dn))
else:
if Nnew_na == Nold_na: #same NA number
if Nnew_data > Nold_data:
cmn.run('cp %s %s' % (fn, dn))
else:
cmn.run('cp %s %s' % (fn, dn))
cmn.run('cd %s; cat *.report > allstat.txt' % ddir)
def separate_by_pair_old(label, fns):
#paired = [i for i in fns if ('_paired' in i) ]
paired = [i for i in fns if ('_pair' in i) or ('_R' in i)]
paired.sort()
if len(paired) != 2:
print('error: wrong number of pairs as %s' % str(paired))
print('from: %s' % str(fns))
print('need to change the label criterion')
sys.exit()
unpaired = set(fns) - set(paired)
#parse each files
newPaired = []
for fn in paired:
if os.path.exists(cmn.lastName(fn)):
cmn.run('unlink %s;' % cmn.lastName(fn))
cmn.run('ln -s %s' % fn)
newPaired.append(cmn.lastName(fn))
singleFn = '%s_single.fq' % label
if cmn.filexist(singleFn):
cmn.run('rm %s' % singleFn)
for fn in unpaired:
cmn.run('cat %s >> %s' % (fn, singleFn))
return newPaired, singleFn
def parse_inserted_gap(ID, seq, label):
fn = 'sampleRun_%s/bait_insertion' % ID
#if cmn.filexist(fn) or ('N' in seq.replace('-', 'N').strip('N')):
if cmn.filexist(fn):
#lines = cmn.file2lines(fn)
#lines = sorted(lines, key=lambda x: int(x.split(',')[0][1:]))
#Ngap = 0
#for line in lines:
# items = line.strip().split()
# Ngap += len(items[-1])
#check what is the right range of sequence
print('runing blast to fix %s' % ID)
checkSeq = seq.replace('-', 'N').strip('N')
fquery = 'tmpInput.fa'
fasta = '>input\n%s\n' % checkSeq
cmn.write_file(fasta, fquery)
dn = 'tmpBr_%s.txt' % label
cmd = 'blastn -query %s -db /project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/all_barcodes_4verify.fa ' % fquery
cmd += '-task blastn-short -dust no -outfmt \'6 qseqid sseqid qstart qend sstart send evalue pident qseq sseq\' -out %s' % dn
cmn.run(cmd)
isFixed = False
for line in cmn.file2lines(dn):
items = line.strip().split()
#print items
qstart, qend, sstart, send = list(map(int, items[2:6]))
if sstart == 1 and send == 658 and qstart == 21:
qseq, sseq = items[-2:]
new = [
char1 for char1, char2 in zip(qseq, sseq) if char2 != '-'
]
if len(new) == 658:
seq = seq[:qstart - 1] + ''.join(new) + seq[qend:]
print('solution found for %s' % ID)
isFixed = True
break
if sstart == 2 and send == 655 and qstart == 22:
qseq, sseq = items[-2:]
new = [
char1 for char1, char2 in zip(qseq, sseq) if char2 != '-'
]
if len(new) == 654:
seq = seq[:qstart - 1] + ''.join(new) + seq[qend:]
print('solution found for %s' % ID)
isFixed = True
break
if not isFixed:
cmn.append_file('%s\t%s\n' % (ID, label), 'cannot_fixed_indel.txt')
return seq
def separate_by_pair_vold(fastqs, wdir):
pdict = {}
mapdict = { }
for fastq in fastqs:
key = '.'.join(cmn.lastName(fastq).split('.')[:-1])
mapdict[key] = fastq
names = list(mapdict.keys())
length = min([len(name) for name in names])
for i in range(length):
checks = [name[:-1-i] for name in names]
count_dict = Counter(checks)
if max(count_dict.values()) == 2: #got paired
for name in names:
key = name[:-1-i]
fn = mapdict[name]
try:
pdict[key].append(fn)
except:
pdict[key] = [fn]
break
if len(pdict) == 0:
print('Error! fastq lib name not recognized, contact Wenlin for help!')
sys.exit()
singleLibs = []
keys = list(pdict.keys())
for key in keys:
libs = pdict[key]
if len(libs) != 2:
singleLibs += libs
del pdict[key]
#print 'paired libs are:'
#for key in pdict:
# print pdict[key]
#print '\nsingle libs are:'
#print ' '.join(singleLibs)
singleFn = '%s/single.fq' % wdir
if cmn.filexist(singleFn):
cmn.run('rm %s' % singleFn)
for fn in singleLibs:
cmn.run('cat %s >> %s' % (fn, singleFn))
return pdict, singleFn
def parse_fqlist(fqlist):
alist = []
for line in cmn.file2lines(fqlist):
label = cmn.lastName(line)
if 'R1' in label:
alist.append(line)
elif 'R2' in label:
alist.append(line)
if len(alist) != 2:
print('Error! can not recoginze fastq names in %s' % fqlist)
cmd = 'touch fastq_error'
cmn.run(cmd)
sys.exit()
return [alist]
def parse_ref(seqDict):
cmn.mkdir('baits')
newDict = {}
for i, name in enumerate(seqDict):
seq = seqDict[name]
fnlabel = 'bait%s' % i
dn = 'baits/%s.fa' % fnlabel
name = name.replace('*', '').replace('"', "'")
fasta = '>%s\n%s\n' % (name, seq)
cmn.write_file(fasta, dn)
cmd = 'module add bwa; bwa index %s -p %s' % (dn, fnlabel)
cmn.run(cmd)
newDict[name] = dn
return newDict
def get_mash_file(name, seq):
global mash_file_dict, cpu
try:
fn = mash_file_dict[name]
except KeyError:
fn = '/tmp/%s' % name
seq = ''.join(seq).replace('-', '').replace('N', '')
fasta = '>%s\n%s\n' % (name, seq)
cmn.write_file(fasta, fn)
cmd = '/home2/wli/local/mash-Linux64-v1.1.1/mash sketch -n -p %s %s' % (
cpu, fn)
cmn.run(cmd)
dn = fn + '.msh'
mash_file_dict[name] = dn
fn = dn
return fn
def do_barcode_blast(sequence, seqDict):
#fref = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/species_barcodes_4mapping.fa'
#fadd = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/added_from_customBaits.baitInfo'
fdb = makeBlastDatabase(seqDict)
#fdb = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/all_barcodes_NoN_0.95.fasta'
namelabel = sequence.split()[0][1:].split()[0].split('|')[0].replace('*','').split('[')[0].replace('"','').replace("'", '')
namelabel = namelabel.replace('/', '_')
fquery = '/tmp/%s.fa' % namelabel
cmn.write_file(sequence, fquery)
cmd = 'module add blast; blastn -query %s -db %s ' % (fquery, fdb)
cmd += '-outfmt \'6 sseqid qlen slen length pident\''
lines = cmn.cmd2lines(cmd)
cmn.run('rm %s' % fquery)
return lines
def merge_sams(dn, fns):
#dn = '%s.sam' % label
print('merging files: %s into %s' % (str(fns), dn))
if cmn.filexist(dn):
cmn.run('rm ' + dn)
fp_dn = open(dn, "a")
filter_and_write_lines(fp_dn, fns[0], header=True)
for fn in fns[1:]:
filter_and_write_lines(fp_dn, fn)
fp_dn.close()
return dn
def do_barcode_blast(sequence):
fdb = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/all_barcodes_4verify.fa'
namelabel = sequence.split()[0][1:].split()[0].split('|')[0].replace(
'*', '').split('[')[0].replace('"', '').replace(
"'", '').split('(')[0].split('/')[0].split('\\')[0]
fquery = '/tmp/%s.fa' % namelabel
cmn.write_file(sequence, fquery)
fbr = fquery + '.br'
cmd = 'module add blast; blastn -max_target_seqs 1000 -query %s -db %s -ungapped ' % (
fquery, fdb)
cmd += '-outfmt \'6 sseqid slen length pident qstart qend qseq sseq\''
cmd += ' -out %s ' % fbr
#print cmd
cmn.run(cmd)
#cmd += ' | head -n 10'
#lines = cmn.cmd2lines(cmd)
lines = cmn.file2lines(fbr)
cmn.run('rm %s' % fquery)
return lines
def extract_same_genus(genus, fall):
dn = 'genus_for_autoPicking.fa'
namelist = []
with open(fall) as fp, open(dn, 'w') as dp:
for line in fp:
if '>' in line:
name = line[1:].strip()
label = name.split('_')[0]
if label == genus:
isGood = True
namelist.append(name)
else:
isGood = False
if isGood:
dp.write(line)
cmd = 'module add bwa; bwa index %s' % dn
cmn.run(cmd)
return dn, namelist
def merge_sams(label, fns):
dn = '%s.sam' % label
print('merging files: %s into %s' % (str(fns), dn))
if cmn.filexist(dn):
cmn.run('rm ' + dn)
cmn.run('cp %s %s' % (fns[0], dn))
fp_dn = open(dn, "a")
for fn in fns[1:]:
fp = open(fn)
for line in fp:
if line[0] != "@" and line[0] != "[" and line.split()[2] != "*":
#if line[0] != "@":
fp_dn.write(line)
fp.close()
fp_dn.close()
return dn
def separate_by_pair(label, fns):
paired = [i for i in fns if ('_paired' in i) or ('_R' in i)]
paired.sort()
if len(paired) != 2:
print('error: wrong number of pairs as %s' % str(paired))
print('from: %s' % str(fns))
#print 'need to change the label criterion'
print('skip this lib')
return None, None
unpaired = set(fns) - set(paired)
#parse each files
newPaired = []
for fn in paired:
cmn.run('ln -s %s' % fn)
newPaired.append(cmn.lastName(fn))
singleFn = '%s_single.fq' % label
if cmn.filexist:
cmn.run('rm %s' % singleFn)
for fn in unpaired:
cmn.run('cat %s >> %s' % (fn, singleFn))
return newPaired, singleFn
def backup_vcf_coverage(wdir):
ddir = '/project/biophysics/Nick_lab/mtang/archive/step4_postprocessing/check_vcf_coverage'
fns = cmn.cmd2lines('ls %s/*_vcf.cov' % wdir)
#1. only back up the new version of cov file
for fn in fns:
print('processing %s...' % fn)
lines = cmn.file2lines(fn)
items = lines[-1].strip().split()
if len(items) != 6:
print('skip old format file %s' % fn)
continue
fnlabel = cmn.lastName(fn)
dn = '%s/%s' % (ddir, fnlabel)
if os.path.exists(dn):
print('merging new and old data for %s' % fnlabel)
covOld = float(cmn.file2lines(dn)[-1].split()[-2])
cov = float(lines[-1].split()[-2])
if cov > covOld:
cmn.run('cp %s %s' % (fn, dn))
else:
cmn.run('cp %s %s' % (fn, dn))
def grep_reads(read, f_libs, direction):
#reverse the read
#reverse = ''.join([rdict[i] for i in read[::-1]])
cmds = []
for fn in f_libs:
cmd = '/project/biophysics/Nick_lab/wli/sequencing/scripts/grep_reads.py %s %s %s &' % (
read, fn, direction)
cmds.append(cmd)
cmds.append('\nwait;\n')
f_job = 'grep_read.job'
cmn.write_lines(cmds, f_job)
cmn.run('bash %s ' % f_job)
#the output dir is grep_out
dn = 'all_grep_reads.txt'
cmn.run('cat grep_out/* > %s' % dn)
fished_reads = cmn.getid(dn)
return fished_reads
def backup_fasta(wdir):
ddir = '/project/biophysics/Nick_lab/mtang/archive/step4_postprocessing/map2fasta'
fns = cmn.cmd2lines('ls %s/*_m2s.fa| grep -v all_genome' % wdir)
for fn in fns:
print('processing %s...' % fn)
fnlabel = cmn.lastName(fn)
#don't back up the ones without species
items = fnlabel.replace('_snp_step2_MITO_m2s.fa',
'').replace('_snp_step2_m2s.fa', '').split('_')
if len(items) == 1:
print('skip the fasta without sp for %s' % fn)
continue
#get the least gapped one
dn = '%s/%s' % (ddir, fnlabel)
if os.path.exists(dn):
print('merging new and old data for %s' % fnlabel)
Nold = count_fasta_nonGap(dn)
Nnew = count_fasta_nonGap(fn)
if Nnew > Nold:
cmn.run('cp %s %s' % (fn, dn))
else:
cmn.run('cp %s %s' % (fn, dn))
def attempt_to_find_genus_by_abundence(ID, fqlist):
tmpdir = 'tmp_%s' % ID
cmn.mkdir(tmpdir)
os.chdir(tmpdir)
cmn.write_lines(fqlist, 'fqlist')
cmd = '/work/archive/biophysics/Nick_lab/wli/project/sequencing/scripts/barcode_scripts/auto_rebait.py fqlist'
cmn.run(cmd)
dn = 'picked_bait.txt'
if cmn.filexist(dn):
genus = cmn.txt_read(dn).strip().split('_')[0].split()[0]
else:
genus = None
os.chdir('..')
cmn.run('cp %s/mapping_stat.info tmpStat/%s_mapping_stat.info' % (tmpdir, ID))
cmn.run('rm -r %s ' % tmpdir)
return genus
print("Usage: *.py fa Ncores", file=sys.stderr)
sys.exit()
#if the nodes are less than 4 taxa, produce a random tree
cmd = "grep '>' %s" % (fn)
lines = [
each[1:].strip() for each in cmn.cmd2lines(cmd) if each.strip() != ''
]
N = len(lines)
if N < 4:
print('Warning: fastme can not make tree of less than 4 taxa')
print('Warning: so I make a fake tree...')
dn = '%s.phylip.fastme.tre' % cmn.lastName(fn)
if N == 1:
info = '(%s);\n' % lines[0]
if N == 2:
a, b = lines
info = '(%s,%s);\n' % (a, b)
elif N == 3:
a, b, c = lines
info = '((%s,%s),%s);\n' % (a, b, c)
cmn.write_file(info, dn)
sys.exit()
label = cmn.lastName(fn)
cmd = 'rm RAxML_*.%s;' % label
cmd += '/home2/wli/local/RAxML/raxmlHPC-PTHREADS-SSE3 -m GTRGAMMA -p 7112 -T %s -s %s -n %s' % (
Ncores, label, label)
cmn.run(cmd)
info = info.replace('[WL_preprocessing]', '\n'.join(step1cmds))
#make snp call cmds
#f_sam = merge_sams(sp, fsams)
info = info.replace('5328', sp)
info = info.replace('[WL_cwd]', os.getcwd())
info2 = template2.replace('assembly_selfref', asslabel)
info2 = info2.replace('5328', sp)
info2 = info2.replace('[WL_cwd]', os.getcwd())
os.chdir('..')
fjob = 'job_files/s1_%s.job' % sp
cmn.write_file(info, fjob)
cmn.run('cd job_files; sbatch s1_%s.job' % sp)
if sp not in step1_finished:
step1_jobs.append(fjob)
fjob = 'job_files/s2_%s.job' % sp
cmn.write_file(info2, fjob)
step2_jobs.append(fjob)
#cmn.run('cd job_files; sbatch sg%s.job' % sp)
info = ['bash %s\n' % each for each in step1_jobs]
cmn.write_file(''.join(info), 'step1todo.cmds')
info = ['sbatch %s\n' % each for each in step2_jobs]
cmn.write_file(''.join(info), 'step2todo.cmds')
header = lines[0].split()[2:]
#cmn.write_lines(header, 'header_names')
#new = [' '.join(['sp%s' % i for i in xrange(len(header))])]
new = [' '.join(header)]
for line in lines[1:]:
firstChar = ''
items = line.split()[2:]
newline = []
for item in items:
chars = item.split()
if firstChar == '':
firstChar = chars[0]
if len(chars) == 1:
if chars[0] == '-':
newline.append('0,0')
elif firstChar == chars[0]:
newline.append('1,0')
else:
newline.append('0,1')
else: #have both char
newline.append('1,1')
new.append(' '.join(newline))
dn = fn + '.tmix'
cmn.write_lines(new, dn)
cmn.run('gzip %s' % dn)
for sample in groupDict:
fqlist = groupDict[sample]
#fqlist = cmn.cmd2lines('ls /project/biophysics/Nick_lab/wli/sequencing/Eudamine/BEAST_timing/tmp_link_fastq/%s*.fastq' % sample)
#fqlist = cmn.cmd2lines('ls /work/biophysics/wli/workspace/filtered_6313*q')
wdir = 'mitoD_%s' % sample
cmn.mkdir(wdir)
os.chdir(wdir)
cwd = os.getcwd()
info = template.replace('[cwd]', cwd)
info = info.replace('[fq_files]', ' '.join(fqlist))
info = info.replace('[sample]', sample)
#prepare quake infiles
fqlist_local = []
for fq in fqlist:
cmn.run('ln -s ' + fq)
fqlist_local.append(cmn.lastName(fq))
cmn.write_lines(fqlist_local, 'fqlist')
cmn.run('ln -s fqlist infiles')
#make fq2fa comand
quake_fqlist = [each.replace('.fastq', '.cor.fastq') for each in fqlist_local]
fq2fa_cmds = ['rm %s.fa 2> /dev/null' % sample]
for fq in quake_fqlist:
cmd = 'fq2fa %s >> %s.fa;' % (fq, sample)
fq2fa_cmds.append(cmd)
cmn.write_lines(quake_fqlist, 'fqlist.cor')
cmd = '\n'.join(fq2fa_cmds)
info = info.replace('[fq2fa_commands]', cmd)