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#!/usr/bin/python3
"""
A reader of SAM format.
import samreader
# ...
# Attach it to stdin and print the header.
sam_reader = SamReader(sys.stdin)
print sam_reader.header
# ...
# Open a SAM file and store each read starting position.
with fopen(myfile) as fp:
sr = SamReader(fp)
for rec in sr:
start_coord[rec.qname] = rec.pos
"""
class CigarString(object):
"""
A basic Cigar.
"""
def __init__(self, cigar):
self.cigar = cigar
self.set_idx = 0
def __str__(self):
return self.cigar
class SamHeader(object):
"""
Sam Header.
"""
def __init__(self, file_handler):
self.header_lines = list()
self.curr_idx = 0
self._source_fh = file_handler
self.end_header_pointer = self._load_header()
def __iter__(self):
self.curr_idx = 0
return self
def __next__(self):
if self.curr_idx == len(self.header_lines):
raise StopIteration
value = self.header_lines[self.curr_idx]
self.curr_idx += 1
return value
def __str__(self):
return "\n".join(self.header_lines)
def _load_header(self):
fh = self._source_fh
fh.seek(0)
last_pos = fh.tell()
line = fh.readline().rstrip()
while line[0] == '@':
self.header_lines.append(line)
last_pos = fh.tell()
line = fh.readline().rstrip()
fh.seek(last_pos)
return last_pos
class SamRecord(object):
"""
Record Item for SAM.
"""
def __init__(self, sam_line):
all_tokens = sam_line.rstrip().split('\t')
# NOTE: not care about optional fields for now.
self.rec_keys = ['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'RNEXT', 'PNEXT', 'TLEN', 'SEQ', 'QUAL']
rec = {k: all_tokens[i] for i, k in enumerate(self.rec_keys)}
rec['POS'] = int(rec['POS'])
rec['MAPQ'] = int(rec['MAPQ'])
rec['CIGAR'] = CigarString(rec['CIGAR'])
rec['PNEXT'] = int(rec['PNEXT'])
rec['TLEN'] = int(rec['TLEN'])
self.record = rec
self.pos = rec['POS']
self.qname = rec['QNAME']
self.mapq = rec['MAPQ']
self.rname = rec['RNAME']
self.flag = int(rec['FLAG'])
def __str__(self):
return "\t".join([str(self.record[self.rec_keys[i]]) for i in range(len(self.rec_keys))])
class SamReader(object):
"""
Iterable for all SAM records.
"""
def __init__(self, file_handle):
self._source_fh = file_handle
self.header = SamHeader(file_handle)
def __iter__(self):
self._source_fh.seek(self.header.end_header_pointer)
return self
def __next__(self):
line = self._source_fh.readline()
if not line:
raise StopIteration
return SamRecord(line)
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