def __init__(self, num, refname, dbsnpname):
sys.stderr.write('Note: MismatchRefDbSNP is considered *experimental*\n')
self.num = int(num)
self.refname = refname
self.dbsnp = DBSNP(dbsnpname)
if not os.path.exists('%s.fai' % refname):
pysam.faidx(refname)
self.ref = pysam.Fastafile(refname)
def __init__(self, num, fname, verbose=None):
sys.stderr.write('Note: MismatchDbSNP is considered *experimental*\n')
self.num = int(num)
self.fname = fname
self.dbsnp = DBSNP(fname)
if verbose == 'verbose':
self.verbose = True
else:
self.verbose = False
class MismatchDbSNP(object):
def __init__(self, num, fname, verbose=None):
sys.stderr.write('Note: MismatchDbSNP is considered *experimental*\n')
self.num = int(num)
self.fname = fname
self.dbsnp = DBSNP(fname)
if verbose == 'verbose':
self.verbose = True
else:
self.verbose = False
def filter(self, bam, read):
if read.is_unmapped:
return False
if read_calc_mismatches(read) <= self.num:
return True
chrom = bam.getrname(read.tid)
mm = 0
snps = 0
for op, pos, seq in read_calc_variations(read):
if not self.dbsnp.is_valid_variation(chrom, op, pos, seq,
self.verbose):
mm += 1
else:
snps += 1
if mm > self.num:
return False
if snps:
read.tags = read.tags + [('ZS', snps)]
return True
def __repr__(self):
return '>%s mismatch%s using %s' % (self.num, '' if self.num == 1 else
'es', os.path.basename(self.fname))
def close(self):
self.dbsnp.close()
class MismatchRefDbSNP(object):
def __init__(self, num, refname, dbsnpname):
sys.stderr.write(
'Note: MismatchRefDbSNP is considered *experimental*\n')
self.num = int(num)
self.refname = refname
self.dbsnp = DBSNP(dbsnpname)
if not os.path.exists('%s.fai' % refname):
pysam.faidx(refname)
self.ref = pysam.Fastafile(refname)
def filter(self, bam, read):
if read.is_unmapped:
return False
chrom = bam.getrname(read.tid)
mm = 0
snps = 0
for op, pos, seq in read_calc_mismatches_gen(self.ref, read, chrom):
if not self.dbsnp.is_valid_variation(chrom, op, pos, seq):
mm += 1
else:
snps += 1
if mm > self.num:
return False
if snps:
read.tags = read.tags + [('ZS', snps)]
return True
def __repr__(self):
return '>%s mismatch%s using %s/%s' % (
self.num, '' if self.num == 1 else 'es',
os.path.basename(self.dbsnpname), os.path.basename(self.refname))
def close(self):
self.ref.close()
self.dbsnp.close()
def __init__(self, num, refname, dbsnpname):
sys.stderr.write('Note: MismatchRefDbSNP is considered *experimental*\n')
self.num = int(num)
self.refname = refname
self.dbsnp = DBSNP(dbsnpname)
if not os.path.exists('%s.fai' % refname):
pysam.faidx(refname)
self.ref = pysam.Fastafile(refname)
def __init__(self, num, fname, verbose=None):
sys.stderr.write('Note: MismatchDbSNP is considered *experimental*\n')
self.num = int(num)
self.fname = fname
self.dbsnp = DBSNP(fname)
if verbose == 'verbose':
self.verbose = True
else:
self.verbose = False
class MismatchDbSNP(object):
def __init__(self, num, fname, verbose=None):
sys.stderr.write('Note: MismatchDbSNP is considered *experimental*\n')
self.num = int(num)
self.fname = fname
self.dbsnp = DBSNP(fname)
if verbose == 'verbose':
self.verbose = True
else:
self.verbose = False
def filter(self, bam, read):
if read.is_unmapped:
return False
if read_calc_mismatches(read) <= self.num:
return True
chrom = bam.getrname(read.tid)
mm = 0
snps = 0
for op, pos, seq in read_calc_variations(read):
if not self.dbsnp.is_valid_variation(chrom, op, pos, seq, self.verbose):
mm += 1
else:
snps += 1
if mm > self.num:
return False
if snps:
read.tags = read.tags + [('ZS', snps)]
return True
def __repr__(self):
return '>%s mismatch%s using %s' % (self.num, '' if self.num == 1 else 'es', os.path.basename(self.fname))
def close(self):
self.dbsnp.close()
class MismatchRefDbSNP(object):
def __init__(self, num, refname, dbsnpname):
sys.stderr.write('Note: MismatchRefDbSNP is considered *experimental*\n')
self.num = int(num)
self.refname = refname
self.dbsnp = DBSNP(dbsnpname)
if not os.path.exists('%s.fai' % refname):
pysam.faidx(refname)
self.ref = pysam.Fastafile(refname)
def filter(self, bam, read):
if read.is_unmapped:
return False
chrom = bam.getrname(read.tid)
mm = 0
snps = 0
for op, pos, seq in read_calc_mismatches_gen(self.ref, read, chrom):
if not self.dbsnp.is_valid_variation(chrom, op, pos, seq):
mm += 1
else:
snps += 1
if mm > self.num:
return False
if snps:
read.tags = read.tags + [('ZS', snps)]
return True
def __repr__(self):
return '>%s mismatch%s using %s/%s' % (self.num, '' if self.num == 1 else 'es', os.path.basename(self.dbsnpname), os.path.basename(self.refname))
def close(self):
self.ref.close()
self.dbsnp.close()
