def merge_into_hash(read_prefix, bin_prefix, s, out_path):
H = (c_uint8 * 2**s)()
bin_files = glob.glob(os.path.join(bin_path, 'part-*'))
read_files = [
read_prefix + '.short.singleton.fastq',
read_prefix + '.short.pairs.fastq'
]
for bf in bin_files:
Read_Bin_Index = index_bin_file(bf)
for rf in read_files:
f = open(rf, 'r')
last = None
while last != f.tell():
last = f.tell()
read_strings = read_until_new(f)
if read_strings:
if read_strings[0].strip() in Read_Bin_Index:
read_bins = [
int(rb) for rb in Read_Bin_Index[
read_strings[0].strip()].split(',')
]
for rb in read_bins:
H[rb] = min(255, H[rb] + 1)
f.close()
f0 = open(out_path, 'wb')
f0.write(H)
f0.close()
return H
def merge_files(bin_path,read_path,out_prefix='/mnt/'):
hash_prefix = 'k, bins: '
bin_files = glob.glob(os.path.join(bin_path,'part-*'))
read_files = glob.glob(os.path.join(read_path,'*.fastq'))
for bf in bin_files:
Read_Bin_Index = index_bin_file(bf)
for rf in read_files:
f = open(rf,'r')
g = open(out_prefix+rf[rf.rfind('/')+1:rf.rfind('.')]+'.hashq','a')
last = None
while last != f.tell():
last = f.tell()
read_strings = read_until_new(f)
if len(read_strings) > 1:
if read_strings[0].strip().split()[0] in Read_Bin_Index:
g.writelines(read_strings)
# SUPER DUMB: HARDCODE WRITING KMER SIZE
g.write(hash_prefix+'[35,'+Read_Bin_Index[read_strings[0].strip().split()[0]][:-1]+']\n')
f.close()
g.close()
print bf,rf
def merge_into_hash(read_prefix,bin_prefix,s,out_path):
H = (c_uint8*2**s)()
bin_files = glob.glob(os.path.join(bin_path,'part-*'))
read_files = [read_prefix+'.short.singleton.fastq',read_prefix+'.short.pairs.fastq']
for bf in bin_files:
Read_Bin_Index = index_bin_file(bf)
for rf in read_files:
f = open(rf,'r')
last = None
while last != f.tell():
last = f.tell()
read_strings = read_until_new(f)
if read_strings:
if read_strings[0].strip() in Read_Bin_Index:
read_bins = [int(rb) for rb in Read_Bin_Index[read_strings[0].strip()].split(',')]
for rb in read_bins:
H[rb] = min(255,H[rb]+1)
f.close()
f0 = open(out_path,'wb')
f0.write(H)
f0.close()
return H
def merge_files(bin_path, read_path, out_prefix='/mnt/'):
hash_prefix = 'k, bins: '
bin_files = glob.glob(os.path.join(bin_path, 'part-*'))
read_files = glob.glob(os.path.join(read_path, '*.fastq'))
for bf in bin_files:
Read_Bin_Index = index_bin_file(bf)
for rf in read_files:
f = open(rf, 'r')
g = open(
out_prefix + rf[rf.rfind('/') + 1:rf.rfind('.')] + '.hashq',
'a')
last = None
while last != f.tell():
last = f.tell()
read_strings = read_until_new(f)
if len(read_strings) > 1:
if read_strings[0].strip().split()[0] in Read_Bin_Index:
g.writelines(read_strings)
# SUPER DUMB: HARDCODE WRITING KMER SIZE
g.write(hash_prefix + '[35,' + Read_Bin_Index[
read_strings[0].strip().split()[0]][:-1] + ']\n')
f.close()
g.close()
print bf, rf
