def parse_mapping_stringent(mapping, assembly, mm, \
ends = False, scaffolds = False, max_cov = 100):
"""
- create a paired-read dictionary from sam files
- only include stringently mapped reads
- use max_cov to limit the number of reads stored
* pairs[read] = [bit, mate, mappping[scaffold] = [map, map2, ...], fastq]
* map = [overlap, mismatches, sam_info]
* sam_info = all sam lines except read + quality
"""
pairs = {}
header = []
# make sure that mapping was successful
if mapping is False:
return pairs, header
# s2c[scaffold] = [[coverage per position, # reads connecting base to the next base], [p2, pn2]]
s2c = {
id: [[0, False, False] for i in range(0, info[1])]
for id, info in list(assembly.items())
}
for line in open(mapping):
if line.startswith('@'):
header.append(line.strip())
continue
line = line.strip().split()
# only include stringently mapped reads
mismatches = map_tool.count_mismatches(line)
if mismatches > mm:
continue
read, bit, scaffold, start = line[0:4]
bit, start = int(bit), int(start)
r = [start, start + len(line[9]) - 1]
# make sure read is > 10 bp long
if r[1] - r[0] < 10:
continue
fastq = map_tool.sam2fastq(line)
info = [line[0:9], line[11:]]
if '/' in read:
read = read.rsplit('/', 1)[0]
if bin(bit)[-7] == '1': # first sequence in pair
read = '%s_1' % (read)
mate = '%s_2' % (read.rsplit('_', 1)[0])
else:
read = '%s_2' % (read)
mate = '%s_1' % (read.rsplit('_', 1)[0])
if ends is not False and (r[0] > ends
and r[1] < scaffolds[scaffold][1] - ends):
continue
if min([i[0] for i in s2c[scaffold][r[0]:r[1]]]) >= max_cov:
continue
s2c = add_coverage(scaffold, assembly, r, s2c, line, window=0)
pairs = add_read(pairs, read, info, r, bit, mate, fastq, mismatches,
scaffold)
return pairs, header
def check_mm(sam, window, read_length):
"""
make sure mismatches are not in window at beginning or end of read
if mismatches are not in the beginning or end of the read, return False
"""
mm = map_tool.count_mismatches(sam)
if mm is False:
return True
if mm == 0:
return False
mm_positions = mm_positions_from_md(sam, read_length)
if mm_positions is False:
return False
elif mm_positions is True:
return True
for pos in mm_positions:
if pos <= window or pos >= (read_length - window):
return True
return False
def parse_mapping_errors(mapping, s2errors, s2windows):
"""
- create a paired-read dictionary from sam files
- only include reads mapping to error window
* pairs[read] = [bit, mate, mappping[scaffold] = [map, map2, ...], fastq]
* map = [overlap, mismatches, sam_info]
* sam_info = all sam lines except read + quality
"""
pairs = {}
for line in open(mapping):
if line.startswith('@'):
continue
line = line.strip().split()
read, bit, scaffold, start = line[0:4]
bit, start = int(bit), int(start)
r = [start, start + len(line[9]) - 1]
m_scaffold = line[6]
if scaffold != m_scaffold:
mate_r = [False, False]
else:
mstart = int(line[7])
mate_r = [mstart, mstart + len(line[9]) - 1]
# make sure read or mate overlaps with an error window
if map2window(scaffold, s2windows, s2errors, r, mate_r) is False:
continue
mismatches = map_tool.count_mismatches(line)
fastq = map_tool.sam2fastq(line)
info = [line[0:9], line[11:]]
if '/' in read:
read = read.rsplit('/', 1)[0]
if bin(bit)[-7] == '1': # first sequence in pair
read = '%s_1' % (read)
mate = '%s_2' % (read.rsplit('_', 1)[0])
else:
read = '%s_2' % (read)
mate = '%s_1' % (read.rsplit('_', 1)[0])
pairs = add_read(pairs, read, info, r, bit, mate, fastq, mismatches,
scaffold)
return pairs
def parse_mapping(mapping, ends = False, scaffolds = False):
"""
create a paired-read dictionary from sam files
* pairs[read] = [bit, mate, mappping[scaffold] = [map, map2, ...], fastq]
* map = [overlap, mismatches, sam_info]
* sam_info = all sam lines except read + quality
"""
pairs = {}
header = []
for line in open(mapping):
if line.startswith('@'):
header.append(line.strip())
continue
line = line.strip().split()
read, bit, scaffold, start = line[0:4]
bit, start = int(bit), int(start)
r = [start, start + len(line[9]) - 1]
mismatches = map_tool.count_mismatches(line)
fastq = map_tool.sam2fastq(line)
info = [line[0:9], line[11:]]
if '/' in read:
read = read.rsplit('/', 1)[0]
if bin(bit)[-7] == '1': # first sequence in pair
read = '%s_1' % (read)
mate = '%s_2' % (read.rsplit('_', 1)[0])
else:
read = '%s_2' % (read)
mate = '%s_1' % (read.rsplit('_', 1)[0])
if ends is not False and (r[0] > ends and r[1] < scaffolds[scaffold][1] - ends):
continue
if read not in pairs:
pairs[read] = [bit, mate, {}, fastq]
if scaffold not in pairs[read][2]:
pairs[read][2][scaffold] = []
pairs[read][2][scaffold].append([r, mismatches, info])
return pairs, header
def copies(mapping, s2bins, rna, min_rna=800, mismatches=0):
"""
1. determine bin coverage
2. determine rRNA gene coverage
3. compare
"""
cov = {} # cov[scaffold] = [bases, length]
s2bins, bins2s = parse_s2bins(s2bins)
rna_cov = parse_rna(rna, s2bins, min_rna)
s2bins, bins2s = filter_missing_rna(s2bins, bins2s, rna_cov)
# count bases mapped to scaffolds and rRNA gene regions
for line in mapping:
line = line.strip().split()
# get scaffold lengths
if line[0].startswith('@'):
if line[0].startswith('@SQ') is False:
continue
s = line[1].split(':')[1]
l = int(line[2].split(':')[1])
# check if scaffold is binned
if s not in s2bins:
continue
if s not in cov:
cov[s] = [0, l]
# check mismatch threshold
mm = count_mismatches(line)
if mm is False or mm > mismatches:
continue
# check that scaffold is in bin
s, bases = line[2], len(line[9])
if s not in cov:
continue
cov[s][0] += bases
rna_cov = rna_bases(rna_cov, s, bases, line)
print('# mismatches threshold: %s' % (mismatches))
header = ['#rRNA scaffold', 'rRNA genes >=%sbp on scaffold' % (min_rna), \
'rRNA coverage', \
'bin', 'bin info', 'bin coverage', \
'rRNAs >=%sbp in bin' % (min_rna), \
'rRNA coverage/bin coverage', \
'estimated number of copies']
print('\t'.join(header))
for bin, scaffolds in list(bins2s.items()):
rna_count = sum(
[len(rna_cov[s][2]) for s in scaffolds if s in rna_cov])
for s in scaffolds:
if s not in rna_cov:
continue
out = []
counts = rna_cov[s]
bin_cov = calc_bin_cov(bins2s[bin], cov)
num_genes = len(counts[2])
rna_coverage = float(float(counts[0]) / float(counts[1]))
if bin_cov == 0:
rna_div_bin = 0
else:
rna_div_bin = float(rna_coverage / bin_cov)
est = int(max([rna_count, counts, rna_div_bin]))
out = [
s, num_genes, rna_coverage, bin, bin_cov, rna_count,
rna_div_bin, est
]
print('\t'.join([str(i) for i in out]))