def rrbs_trim(read, read_info, site_meth_list, single_on, remove_overlap, record_mate, filter_MspI_end_repaired_bp,
filter_remove_overlap_bp, out):
if single_on:
strand, chr, pos1, CIGAR, seq, score = read_info[1], read_info[2], int(read_info[3]) - 1, read_info[4], \
read_info[5], read_info[6]
pos_list = [pos1]
else:
strand, chr, pos1, CIGAR, pos2, insert, seq, score = \
read_info[1], read_info[2], int(read_info[3]) - 1, read_info[4], int(read_info[5]) - 1, abs(
int(read_info[6])), read_info[7], read_info[8]
if pos2 < pos1 and (strand == '++' or strand == '--') or (pos1 < pos2 and (strand == '+-' or strand == '-+')):
out.write(read)
return record_mate, filter_MspI_end_repaired_bp, filter_remove_overlap_bp
pos_list = [pos1, pos2]
reverse_strand = ['-+', '+-']
original_read_info = read.rstrip().split('\t')
seq, score, filter_MspI_end_repaired_bp, CIGAR, pos_list = get_filted_info(strand, seq, score, CIGAR, site_meth_list, single_on, reverse_strand,
filter_MspI_end_repaired_bp, pos_list)
##output the trimming result
if single_on:
pos1 = pos_list[0]
out.write('%s\t%s\t%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s'
% (original_read_info[0], original_read_info[1], original_read_info[2], pos1, original_read_info[4],
CIGAR, original_read_info[6], original_read_info[7], original_read_info[8], seq, score))
for i in range(11, len(original_read_info)):
out.write('\t%s' % original_read_info[i])
out.write('\n')
else:
#get the original information
pos1, pos2 = pos_list[0], pos_list[1]
strand, chr, pos1_ori, pos2_ori, insert = \
read_info[1], read_info[2], int(read_info[3]) - 1, int(read_info[5]) - 1, abs(int(read_info[6]))
if strand in reverse_strand:
site_information = [chr, str(pos2_ori), str(pos1_ori), str(insert)] #change pos2 and pos1 in '+-' or '-+'
else:
site_information = [chr, str(pos1_ori), str(pos2_ori), str(insert)]
read_mate_site = '_'.join(site_information)
p_dict = {'++': '+-', '+-': '++', '-+': '--', '--': '-+'}
if not record_mate.has_key(read_mate_site):
record_mate[read_mate_site] = [[read, strand, CIGAR, seq, score, pos1, pos2]]
else:
record_mate[read_mate_site].append([read, strand, CIGAR, seq, score, pos1, pos2])
if len(record_mate[read_mate_site]) == 2 and p_dict[record_mate[read_mate_site][0][1]] == \
record_mate[read_mate_site][1][1]:
#get the new position
for mate in record_mate[read_mate_site]:
if mate[1] not in reverse_strand:
if mate[5] > mate[6]: ####fix the rrbs paired-end bug 2014-04
pos1_new = mate[6]
pos2_new = mate[6]
else:
pos1_new = mate[5]
pos2_new = mate[6]
#get new insert
for mate in record_mate[read_mate_site]:
if mate[1] in reverse_strand:
insert = pos2_new - pos1_new + len(mate[3])
for mate in record_mate[read_mate_site]:
read, strand, CIGAR, seq, score = mate[0], mate[1], mate[2], mate[3], mate[4]
if remove_overlap:
if strand not in reverse_strand:
CIGAR, seq, score, filter_remove_overlap_bp = PF.remove_overlap_seq(pos1_new, pos2_new,
insert, seq, score,
CIGAR,
filter_remove_overlap_bp)
if len(seq) == 0:
#In this situation, the two read mates are the same, we should count one time if remove_overlap is True
continue
else:
PF.writer(pos1_new, CIGAR, pos2_new, insert, seq, score, read, out)
else:
PF.writer(pos2_new, CIGAR, pos1_new, -insert, seq, score, read, out)
else:
if strand not in reverse_strand:
PF.writer(pos1_new, CIGAR, pos2_new, insert, seq, score, read, out)
else:
PF.writer(pos2_new, CIGAR, pos1_new, -insert, seq, score, read, out)
del record_mate[read_mate_site]
return record_mate, filter_MspI_end_repaired_bp, filter_remove_overlap_bp
def nonuniform_filter(read, out, read_info, ref, remove_overlap, duplicate, single_on, record_mate, trim_position, filter_nonuniform_trim_bp_CG,
filter_duplicate_reads, filter_remove_overlap_bp):
'''
Use the strategy in Bis-SNP to trim 5' bisulfite conversion failures
For each read, we walk along the read from 5' to 3',
and we remove any Cs on the C-strand until we reach the first reference C which is converted to a T.
'''
#if the read is duplicate read and the --filter_dup has been set True, the read will be removed
if duplicate:
filter_duplicate_reads += 1 ##record the duplicate read (2013-06-20)
return record_mate, trim_position, filter_nonuniform_trim_bp_CG, filter_duplicate_reads, filter_remove_overlap_bp
if single_on:
strand, chr, pos1, CIGAR, seq, score = read_info[1], read_info[2], int(read_info[3]) - 1, read_info[4], \
read_info[5], read_info[6]
else:
strand, chr, pos1, CIGAR, pos2, insert, seq, score = \
read_info[1], read_info[2], int(read_info[3]) - 1, read_info[4], int(read_info[5]) - 1, abs(
int(read_info[6])), read_info[7], read_info[8]
if pos2 < pos1 and (strand == '++' or strand == '--') or (pos1 < pos2 and (strand == '+-' or strand == '-+')):
out.write(read)
return record_mate, trim_position, filter_nonuniform_trim_bp_CG, filter_duplicate_reads, filter_remove_overlap_bp
BS_conversion = {'+': ('C', 'T'), '-': ('G', 'A')}
reverse_strand = ['-+', '+-']
original_read_info = read.rstrip().split('\t')
#filter 5' conversion failure read by read
readlen = len(seq)
refseq = ref[chr][pos1:pos1 + readlen]
refseq_for_trim = ref[chr][pos1 - 1:pos1 + readlen + 1]
# if the strand is '-+' (single-end) or '+-', reverse the seq and refseq
if strand in reverse_strand:
seq = seq[::-1]
refseq = refseq[::-1]
score = score[::-1]
match, convert = BS_conversion[strand[0]]
index = refseq.find(match) #record the position
while index >= 0:
if seq[index] == convert:
break
else:
index = refseq.find(match, index + 1)
if index < 0: #no finding C or G
index = 0
if index < len(trim_position):
trim_position[index] += 1
else:
new_trim_position = [0] * ((index + 1) - len(trim_position))
trim_position = trim_position + new_trim_position
trim_position[index] += 1
#trimming
if strand in reverse_strand:
seq = seq[index:][::-1]
score = score[index:][::-1]
pos1 += 1
if not single_on:
pos2 += 1
else:
seq = seq[index:]
score = score[index:]
pos1 = pos1 + index + 1
if not single_on:
pos2 += 1
CIGAR = str(len(seq)) + CIGAR[-1]
if strand in reverse_strand:
refseq_trim = refseq_for_trim[len(seq):]
else:
refseq_trim = refseq_for_trim[:index + 2]
filter_nonuniform_trim_bp_CG = PF.get_trim_CG(refseq_trim, strand, filter_nonuniform_trim_bp_CG)
if single_on:
out.write('%s\t%s\t%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s'
% (original_read_info[0], original_read_info[1], original_read_info[2], pos1, original_read_info[4],
CIGAR, original_read_info[6], original_read_info[7], original_read_info[8], seq, score))
for i in range(11, len(original_read_info)):
out.write('\t%s' % original_read_info[i])
out.write('\n')
else:
#get the original information
strand, chr, pos1_ori, pos2_ori, insert = \
read_info[1], read_info[2], int(read_info[3]) - 1, int(read_info[5]) - 1, abs(int(read_info[6]))
if strand in reverse_strand:
site_information = [chr, str(pos2_ori), str(pos1_ori), str(insert)] #change pos2 and pos1 in '+-' or '-+'
else:
site_information = [chr, str(pos1_ori), str(pos2_ori), str(insert)]
read_mate_site = '_'.join(site_information)
p_dict = {'++': '+-', '+-': '++', '-+': '--', '--': '-+'}
if not record_mate.has_key(read_mate_site):
record_mate[read_mate_site] = [[read, strand, CIGAR, seq, score, pos1, pos2]]
else:
record_mate[read_mate_site].append([read, strand, CIGAR, seq, score, pos1, pos2])
if len(record_mate[read_mate_site]) == 2 and p_dict[record_mate[read_mate_site][0][1]] == \
record_mate[read_mate_site][1][1]:
#get the new position
for mate in record_mate[read_mate_site]:
if mate[1] not in reverse_strand:
pos1_new = mate[5]
pos2_new = mate[6]
#get new insert
for mate in record_mate[read_mate_site]:
if mate[1] in reverse_strand:
insert = pos2_new - pos1_new + len(mate[3])
for mate in record_mate[read_mate_site]:
read, strand, CIGAR, seq, score = mate[0], mate[1], mate[2], mate[3], mate[4]
if remove_overlap:
if strand not in reverse_strand:
CIGAR, seq, score, filter_remove_overlap_bp = PF.remove_overlap_seq(pos1_new, pos2_new,
insert, seq, score,
CIGAR,
filter_remove_overlap_bp)
if len(seq) == 0:
#In this situation, the two read mates are the same, we should count one time if remove_overlap is True
continue
else:
PF.writer(pos1_new, CIGAR, pos2_new, insert, seq, score, read, out)
else:
PF.writer(pos2_new, CIGAR, pos1_new, -insert, seq, score, read, out)
else:
if strand not in reverse_strand:
PF.writer(pos1_new, CIGAR, pos2_new, insert, seq, score, read, out)
else:
PF.writer(pos2_new, CIGAR, pos1_new, -insert, seq, score, read, out)
del record_mate[read_mate_site]
return record_mate, trim_position, filter_nonuniform_trim_bp_CG, filter_duplicate_reads, filter_remove_overlap_bp
def rrbs_trim(read, read_info, site_meth_list, single_on, remove_overlap,
record_mate, filter_MspI_end_repaired_bp,
filter_remove_overlap_bp, out):
if single_on:
strand, chr, pos1, CIGAR, seq, score = read_info[1], read_info[2], int(read_info[3]) - 1, read_info[4], \
read_info[5], read_info[6]
pos_list = [pos1]
else:
strand, chr, pos1, CIGAR, pos2, insert, seq, score = \
read_info[1], read_info[2], int(read_info[3]) - 1, read_info[4], int(read_info[5]) - 1, abs(
int(read_info[6])), read_info[7], read_info[8]
if pos2 < pos1 and (strand == '++' or strand == '--') or (
pos1 < pos2 and (strand == '+-' or strand == '-+')):
out.write(read)
return record_mate, filter_MspI_end_repaired_bp, filter_remove_overlap_bp
pos_list = [pos1, pos2]
reverse_strand = ['-+', '+-']
original_read_info = read.rstrip().split('\t')
seq, score, filter_MspI_end_repaired_bp, CIGAR, pos_list = get_filted_info(
strand, seq, score, CIGAR, site_meth_list, single_on, reverse_strand,
filter_MspI_end_repaired_bp, pos_list)
##output the trimming result
if single_on:
pos1 = pos_list[0]
out.write('%s\t%s\t%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s' %
(original_read_info[0], original_read_info[1],
original_read_info[2], pos1, original_read_info[4], CIGAR,
original_read_info[6], original_read_info[7],
original_read_info[8], seq, score))
for i in range(11, len(original_read_info)):
out.write('\t%s' % original_read_info[i])
out.write('\n')
else:
#get the original information
pos1, pos2 = pos_list[0], pos_list[1]
strand, chr, pos1_ori, pos2_ori, insert = \
read_info[1], read_info[2], int(read_info[3]) - 1, int(read_info[5]) - 1, abs(int(read_info[6]))
if strand in reverse_strand:
site_information = [
chr, str(pos2_ori),
str(pos1_ori), str(insert)
] #change pos2 and pos1 in '+-' or '-+'
else:
site_information = [chr, str(pos1_ori), str(pos2_ori), str(insert)]
read_mate_site = '_'.join(site_information)
p_dict = {'++': '+-', '+-': '++', '-+': '--', '--': '-+'}
if not record_mate.has_key(read_mate_site):
record_mate[read_mate_site] = [[
read, strand, CIGAR, seq, score, pos1, pos2
]]
else:
record_mate[read_mate_site].append(
[read, strand, CIGAR, seq, score, pos1, pos2])
if len(record_mate[read_mate_site]) == 2 and p_dict[record_mate[read_mate_site][0][1]] == \
record_mate[read_mate_site][1][1]:
#get the new position
for mate in record_mate[read_mate_site]:
if mate[1] not in reverse_strand:
if mate[5] > mate[
6]: ####fix the rrbs paired-end bug 2014-04
pos1_new = mate[6]
pos2_new = mate[6]
else:
pos1_new = mate[5]
pos2_new = mate[6]
#get new insert
for mate in record_mate[read_mate_site]:
if mate[1] in reverse_strand:
insert = pos2_new - pos1_new + len(mate[3])
for mate in record_mate[read_mate_site]:
read, strand, CIGAR, seq, score = mate[0], mate[1], mate[
2], mate[3], mate[4]
if remove_overlap:
if strand not in reverse_strand:
CIGAR, seq, score, filter_remove_overlap_bp = PF.remove_overlap_seq(
pos1_new, pos2_new, insert, seq, score, CIGAR,
filter_remove_overlap_bp)
if len(seq) == 0:
#In this situation, the two read mates are the same, we should count one time if remove_overlap is True
continue
else:
PF.writer(pos1_new, CIGAR, pos2_new, insert,
seq, score, read, out)
else:
PF.writer(pos2_new, CIGAR, pos1_new, -insert, seq,
score, read, out)
else:
if strand not in reverse_strand:
PF.writer(pos1_new, CIGAR, pos2_new, insert, seq,
score, read, out)
else:
PF.writer(pos2_new, CIGAR, pos1_new, -insert, seq,
score, read, out)
del record_mate[read_mate_site]
return record_mate, filter_MspI_end_repaired_bp, filter_remove_overlap_bp
