def parse_scaf_length(line):
##contig=<ID=scaffold1_len454574_cov98,length=458273>
adict = {}
scaf = cmn.find_between(line, 'ID=', ',length')
length = int(cmn.find_between(line, ',length=', '>'))
adict[scaf] = length
return adict
def check_difference(seq1, seq2):
print(len(seq1), len(seq2))
if len(seq1) == len(seq2):
return sum([char1 != char2 for char1, char2 in zip(seq1, seq2)
if char1 not in gapChars and char2 not in gapChars])
cmn.write_file(seq1, 'tmpSeq1.fa')
cmn.write_file(seq2, 'tmpSeq2.fa')
info = cmn.cmd2info('blastn -query tmpSeq1.fa -subject tmpSeq2.fa')
#Identities = 656/656 (100%)
identityString = cmn.find_between(info, 'Identities = ', ' (')
identN, totalN = list(map(int, identityString.split('/')))
cmn.write_file(info, 'checkTmp%s.br' % (ID))
return totalN - identN
#different chars and not a gap
seq.append('X')
fasta = '>%s\n%s\n' % (Id, ''.join(seq))
refBaseDict[Id] = ''.join(seq)
new.append(fasta)
cmn.write_file(''.join(new), 'sum_barcodes.fa')
#cmn.run('rm -r sampleRun_fake')
#check denovo pipeline one
fns = cmn.cmd2lines('ls sampleRun_*/denovo_barcode.fa')
denovoDict = {}
new = []
for fn in fns:
Id = cmn.find_between(fn, 'sampleRun_', '/')
lines = cmn.file2lines(fn)
seq = ''.join(lines[1:])
if seq > 658:
tmp = seq.replace('N', '')
if len(tmp) == 658:
seq = tmp
denovoDict[Id] = seq
fasta = '>%s\n%s\n' % (Id, seq)
new.append(fasta)
cmn.write_file(''.join(new), 'sum_denovo.fa')
new = []
for Id in clean_lines:
#options=parse_options()
try:
wdir = sys.argv[1]
except:
print("Usage: *.py t100_highQ", file=sys.stderr)
sys.exit()
cmd = 'grep "Estimated Ln Prob of Data" %s/*/r*/*.log' % wdir
lines = cmn.cmd2lines(cmd)
print('\n'.join(lines))
rdict = {}
countK = {}
for line in lines:
K = cmn.find_between(line, 'structureK', '/')
K = int(K)
lnL = float(line.strip().split()[-1])
try:
rdict[K].append(lnL)
except KeyError:
rdict[K] = [lnL]
try:
countK[K] += 1
except:
countK[K] = 1
keys = list(rdict.keys())
keys.sort()
for K in keys:
if __name__=='__main__':
#options=parse_options()
try:
odir, f_ass = sys.argv[1:3]
except:
print("Usage: *.py filelist assembly_v0.fa", file=sys.stderr)
print("you should index assembly_v0.fa first with -p assembly_v0", file=sys.stderr)
print("using command /home2/wli/local/bwa-0.7.12/bwa index ", file=sys.stderr)
sys.exit()
#fns = cmn.cmd2lines('ls %s/*.fq' % odir)
fns = cmn.getid(odir)
group_dict = separate_by_label(fns)
ass_label = cmn.find_between(cmn.lastName(f_ass), 'assembly_', '.fa')
cmn.mkdir('job_files')
cmn.mkdir('cmd_files')
for plabel in group_dict:
print('processing lib %s' % plabel)
each = group_dict[plabel]
#also parse the files inside this function
#return the file name after parsing
paired, unpaired = separate_by_pair(plabel, each)
if paired == None:
continue
label = '%s_%s' % (plabel, ass_label)
#index_label = cmn.lastName(f_ass).replace('.fa', '')
index_label = f_ass.replace('.fa', '')
try:
fn=sys.argv[1]
except:
print("Usage: *.py link.file", file=sys.stderr)
sys.exit()
dn = 'retrieved_barcodes.fa'
dp = open(dn, 'w')
for link in cmn.file2lines(fn):
if link[0] == '#':
continue
print('processing ' + link)
info = cmn.link2info(link)
seq = cmn.find_between(info, "generateBarcode ('#barcodeImg_", "');").split('\'')[-1]
takeName = False
takeSp = False
for line in info.split('\n'):
if 'Sequence ID' in line:
takeName = True
continue
if '<td>Species:</td>' in line:
takeSp = True
continue
if takeName:
takeName = False
#<td style="width:160px;">ANICE505-10.COI-5P</td>
name = cmn.find_between(line, '>', '<').split('.COI')[0]
if takeSp:
def scaf2numb(scaf):
numb = cmn.find_between(scaf, 'scaffold', '_cov')
return int(numb)
if python_lib not in sys.path:
sys.path.append(python_lib)
import cmn
import requests as rq
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#main
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if __name__ == '__main__':
#options=parse_options()
try:
ID = sys.argv[1]
except:
print("Usage: *.py SRNPnumber", file=sys.stderr)
sys.exit()
url = 'http://janzen.sas.upenn.edu/Wadults/resultsexpressVOUCHB.lasso'
json = {'submitButtonName': 'SUBMIT', 'voucher': ID}
r = rq.post(url, data=json)
sp = cmn.find_between(r.content, 'species:<b>', '</b>').strip()
if '<title>' not in sp:
print(sp)
print("Usage: *.py t100_highQ", file=sys.stderr)
sys.exit()
#cmd = 'grep "Estimated Ln Prob of Data" %s/*/r*/*.log' % wdir
cmd = 'ls %s/*/r*/structure*f' % wdir
fns = cmn.cmd2lines(cmd)
print(fns)
outdir = 'harvest_%s' % wdir
cmn.mkdir(outdir)
cmd_dict = {}
for fn in fns:
#cov_3/structureK10/r0/structure.output_f
K = cmn.find_between(fn, 'structureK', '/')
rep = fn.split('/')[-2]
dn = '%s/out_K%s_%s_f' % (outdir, K, rep)
cmd = 'cp %s %s' % (fn, dn)
try:
cmd_dict[K].append(cmd)
except KeyError:
cmd_dict[K] = [cmd]
for K in cmd_dict:
cmds = cmd_dict[K]
if len(cmds) < 3:
print('insufficent replicates for K=%s, skip' % K)
continue
for cmd in cmds:
cmn.run(cmd)
except:
print("Usage: *.py vcf", file=sys.stderr)
sys.exit()
length_dict = {}
current_scaf = ''
seqDict = {}
order_list = []
with open(fn) as fp:
for line in fp:
line = line.strip()
# ##contig=<ID=scaffold1_cov51,length=30279>
if line.startswith('##contig='):
scaf = cmn.find_between(line, '<ID=', ',')
length = int(cmn.find_between(line, ',length=', '>'))
length_dict[scaf] = length
if line[0] != '#':
items = line.strip().split()
scaf = items[0]
if scaf != current_scaf:
order_list.append(scaf)
#start a new scaffold
expect_index = 1
current_scaf = scaf
else:
expect_index += 1
index = int(items[1])
