def seqblock2alignment(aligned, name, seq):
#tranform the alinged into a dict for better reference
align_dict = {}
for i, j in aligned:
if j != None:
align_dict[j] = i
#subjct_range = [i[1] for i in aligned if i[1]!=None]
#right = max(subjct_range)
#left = min(subjct_range)
right = max(align_dict)
left = min(align_dict)
iLeft = min(align_dict.values())
iRight = max(align_dict.values())
if iRight - iLeft + 1 != len(align_dict):
print('detect deletion!')
cmn.append_file(name + '\n', 'hasDeletion')
iLeft = align_dict[left]
seq = list(seq)
#print aligned
while (iLeft != 0):
iLeft -= 1
left -= 1
#print iLeft
seq[iLeft] = seq[iLeft].lower()
align_dict[left] = iLeft
iRight = align_dict[right]
while (iRight < len(seq) - 1):
iRight += 1
right += 1
seq[iRight] = seq[iRight].lower()
align_dict[right] = iRight
aln = []
for j in range(right):
#j += 1
try:
i = align_dict[j]
if i == None:
char = 'N'
else:
char = seq[i]
except KeyError:
char = '-'
aln.append(char)
return ''.join(aln)
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 get_query_sequence(seqDict, genus, sp):
#1. anything in Eudamine file has higher priority
#fEud = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/Eudaminae-barcode-reference.txt'
#cmd = 'grep %s %s' % (sp, fEud)
#lines = cmn.cmd2lines(cmd)
#if len(lines) == 1:
# name = lines[0].split()[0]
# seq = seqDict[name]
# fasta = '>%s\n%s\n' % (name, seq)
# qlen = len(seq.replace('N', ''))
# print 'pick %s for %s %s' % (name, genus, sp)
# return fasta, qlen
names = list(seqDict.keys())
#try to look up the exact match first
expected_name = '%s_%s' % (genus, sp)
tmp = [name for name in names
if name.upper() == expected_name.upper()]
if len(tmp) != 0:
name = tmp[0]
print('found exact match %s' % name)
seq = seqDict[name]
fasta = '>%s\n%s\n' % (name, seq)
qlen = len(seq.replace('N', ''))
return fasta, qlen
#look it up in other files
good_names = [name for name in names
# if genus.upper() in name.upper().split('_')]
if genus.upper() == name.upper().split('_')[0]]
useGenus = False
if len(good_names) > 0:
useGenus = True
cmn.run('rm pickingLog.txt 2> /dev/null')
if len(good_names) == 0:#sp is just 'sp'
print('can not find barcode for genus keyword "%s"' % genus)
good_names = names
cmn.write_file('noGenus\n', 'pickingLog.txt')
if len(good_names) > 1:
#try to refine it
tmp = [name for name in good_names
if sp.upper() in name.upper().split('_')]
if len(tmp) != 0:
good_names = tmp
else:
cmn.append_file('noSpecies\n', 'pickingLog.txt')
#############################################
####new here, auto pick sequences for those has no info
#############################################
if cmn.filexist('pickingLog.txt'):
print('automatically pick bait by fastq similarity')
fsp = 'restricted_genus.info'
if useGenus and (not cmn.filexist(fsp)):
cmd = '/archive/biophysics/Nick_lab/wli/project/sequencing/scripts/barcode_scripts/auto_rebait.py fqlist %s' % genus
else:
cmd = '/archive/biophysics/Nick_lab/wli/project/sequencing/scripts/barcode_scripts/auto_rebait.py fqlist '
cmn.run(cmd)
good_names = cmn.file2lines('picked_bait.txt')
cmn.write_file('pickClosed\n', 'pickingLog.txt')
#############################################
#############################################
#############################################
#try to see if type species is there
tmp = [name for name in good_names
if name[0] == '*']
if len(tmp) != 0:
good_names = tmp
else:
tmp = [name for name in good_names
if '*' in name]
if len(tmp) != 0:
good_names = tmp
#then randomly pick one, get the max length ones
name = max(good_names, key=lambda x: len(seqDict[x].replace('N', '-')))
#name = name.replace('/', '_')
seq = seqDict[name]
fasta = '>%s\n%s\n' % (name, seq)
qlen = len(seq.replace('N', ''))
print('pick %s for %s %s' % (name, genus, sp))
return fasta, qlen
for fmap in maplist:
sp = cmn.lastName(fmap).split('_')[0]
prot_dict = {}
with open(fmap) as fp:
for i, line in enumerate(fp):
try:
prot = codingI[i]
except KeyError:
continue
#reach here if protein found
a, b = line.strip().split()
try:
prot_dict[prot].append((a, b))
except KeyError:
prot_dict[prot] = [(a, b)]
for prot in prot_dict:
dn = '%s/%s.fa' % (outdir, prot)
alist = prot_dict[prot]
new = []
for i in range(2):
seq = ''.join([each[i] for each in alist])
name = '%s_cp%s' % (sp, i+1)
fasta = '>%s\n%s\n' % (name, seq)
cmn.append_file(fasta, dn)
print('finish processing %s' % fmap)
name, iii, subName = record2name(record)
q = record.qual[i:j]
s = record.seq[i:j]
if iii == 1:
s = reverse_strand(s)
q = q[::-1]
fq = '@%s\n%s\n+\n%s\n' % (subName, s, q)
print(name, subName, i, j, record.seq, s)
if name not in rdict:
rdict[name] = [None, None]
rdict[name][iii] = fq
print('Nbad: %s; Ntotal %s;' % (Nbad, Ntotal))
fq1 = '%s_R1.fq' % outlabel
fq2 = '%s_R2.fq' % outlabel
fsingle = '%s_singleton.fq' % outlabel
for fn in [fq1, fq2, fsingle]:
cmn.run('rm %s' % fn)
for name in rdict:
alist = rdict[name]
if alist.count(None) == 0:
cmn.append_file(alist[0], fq1)
cmn.append_file(alist[1], fq2)
else:
for each in alist:
if each != None:
cmn.append_file(each, fsingle)
cmn.run('rm bait_insertion 2> /dev/null')
hasInsertion = False
for key in indel_dict:
print(key, len(indel_dict[key]))
leftI, rightI = key
cov = (pCoverage[leftI] + pCoverage[rightI]) / 2.0
indel_depth = len(indel_dict[key])
insertion_info = [key, indel_depth, cov]
if indel_depth > 0.5 * cov:
hasInsertion = True
count_dict = Counter(indel_dict[key])
maxChar = max(count_dict, key=lambda x: count_dict[x])
insertion_info.append(maxChar)
insertion_info = '\t'.join(map(str, insertion_info))
cmn.append_file(insertion_info + '\n', 'bait_insertion')
print('insert between ', insertion_info)
for name in bait_names:
bait_dict[name][leftI] += maxChar
#just undergo one round of adding gap
if not hasInsertion:
print('No need to re-run bwa because no insertion in query')
else:
N = cmn.cpu_check()
print('re-run bwa due to insertion')
frefs = update_baits(bait_dict)
fq_groups = group_fq(cmn.file2lines('fqlist'))
def get_query_sequence(seqDict, genus, sp):
#1. anything in Eudamine file has higher priority
#fEud = '/project/biophysics/Nick_lab/wli/sequencing/scripts/data/barcodes/Eudaminae-barcode-reference.txt'
#cmd = 'grep %s %s' % (sp, fEud)
#lines = cmn.cmd2lines(cmd)
#if len(lines) == 1:
# name = lines[0].split()[0]
# seq = seqDict[name]
# fasta = '>%s\n%s\n' % (name, seq)
# qlen = len(seq.replace('N', ''))
# print 'pick %s for %s %s' % (name, genus, sp)
# return fasta, qlen
names = list(seqDict.keys())
#try to look up the exact match first
expected_name = '%s_%s' % (genus, sp)
tmp = [name for name in names if name.upper() == expected_name.upper()]
if len(tmp) != 0:
name = tmp[0]
print('found exact match %s' % name)
seq = seqDict[name]
fasta = '>%s\n%s\n' % (name, seq)
qlen = len(seq.replace('N', ''))
return fasta, qlen
#look it up in other files
good_names = [
name for name in names
# if genus.upper() in name.upper().split('_')]
if genus.upper() == name.upper().split('_')[0]
]
cmn.run('rm pickingLog.txt')
if len(good_names) == 0: #sp is just 'sp'
print('can not find barcode for genus keyword "%s"' % genus)
good_names = names
cmn.write_file('noGenus\n', 'pickingLog.txt')
if len(good_names) > 1:
#try to refine it
tmp = [
name for name in good_names
if sp.upper() in name.upper().split('_')
]
if len(tmp) != 0:
good_names = tmp
else:
cmn.append_file('noSpecies\n', 'pickingLog.txt')
#try to see if type species is there
tmp = [name for name in good_names if name[0] == '*']
if len(tmp) != 0:
good_names = tmp
else:
tmp = [name for name in good_names if '*' in name]
if len(tmp) != 0:
good_names = tmp
#then randomly pick one, get the max length ones
name = max(good_names, key=lambda x: len(seqDict[x].replace('N', '-')))
#name = name.replace('/', '_')
seq = seqDict[name]
fasta = '>%s\n%s\n' % (name, seq)
qlen = len(seq.replace('N', ''))
print('pick %s for %s %s' % (name, genus, sp))
return fasta, qlen