def __init__(self,
ref_fpath,
out_fhand,
length=60,
vcf_fpath=None,
min_length=None):
''''It inits.
The vcf will be used to replace in the reference sequence the SNPs
around the SNP of interest with IUPAC codes
'''
self._sep = u'\t'
self._len = length
if min_length is None:
min_length = length
if min_length > length:
msg = 'Minimum length must be smaller than required length'
raise ValueError(msg)
self._min_len = min_length
self._ref_seqs = seq_index(ref_fpath, format='fasta')
if vcf_fpath:
self._snvs = Reader(filename=vcf_fpath)
else:
self._snvs = None
self._out_fhand = out_fhand
out_fhand.write(u'CHROM\tPOS\tID\tseq\n')
self._prev_chrom = None
def __init__(self, vcf_path, samples=None):
reader = Reader(filename=vcf_path)
self.index = {}
self.samples = samples
for vcf_record in reader:
snp_name = create_snp_name(vcf_record)
self.index[snp_name] = vcf_record
def __init__(self, ref_fpath, out_fhand, length=60, vcf_fpath=None,
min_length=None):
''''It inits.
The vcf will be used to replace in the reference sequence the SNPs
around the SNP of interest with IUPAC codes
'''
self._sep = u'\t'
self._len = length
if min_length is None:
min_length = length
if min_length > length:
msg = 'Minimum length must be smaller than required length'
raise ValueError(msg)
self._min_len = min_length
self._ref_seqs = seq_index(ref_fpath, format='fasta')
if vcf_fpath:
self._snvs = Reader(filename=vcf_fpath)
else:
self._snvs = None
self._out_fhand = out_fhand
out_fhand.write(u'CHROM\tPOS\tID\tseq\n')
self._prev_chrom = None
class IlluminaWriter(object):
'''It writes the SNPs in Illumina format
ref_fpath should be in fasta format and it has to have a name attribute.
min_maf controls the SNPs reported in the adjacent segments as IUPAC codes.
'''
# TODO add extra error classes
# TODO include the error classes inside this class to easy access
class NotEnoughAdjacentSequenceError(Exception):
pass
def __init__(self,
ref_fpath,
out_fhand,
length=60,
vcf_fpath=None,
min_length=None):
''''It inits.
The vcf will be used to replace in the reference sequence the SNPs
around the SNP of interest with IUPAC codes
'''
self._sep = u'\t'
self._len = length
if min_length is None:
min_length = length
if min_length > length:
msg = 'Minimum length must be smaller than required length'
raise ValueError(msg)
self._min_len = min_length
self._ref_seqs = seq_index(ref_fpath, format='fasta')
if vcf_fpath:
self._snvs = Reader(filename=vcf_fpath)
else:
self._snvs = None
self._out_fhand = out_fhand
out_fhand.write(u'CHROM\tPOS\tID\tseq\n')
self._prev_chrom = None
def write(self, snv):
chrom_name = snv.CHROM
prev_chrom = self._prev_chrom
if prev_chrom is None or prev_chrom.name != chrom_name:
chrom = self._ref_seqs[chrom_name]
self._prev_chrom = chrom
else:
chrom = prev_chrom
length = self._len
min_len = self._min_len
snv_start = snv.start # 0 based
snv_end = snv.end # 1 based
desired_start = snv_start - length # desired segment start
end = snv_end + length # desired segment end
chrom_seq = chrom.seq
first_segment = unicode(chrom_seq[desired_start:snv_start])
if len(first_segment) < min_len:
msg = "Not enough sequence in 3'. ID: %s, POS: %d, CHROM: %s"
msg %= (snv.ID, snv.POS, snv.CHROM)
raise self.NotEnoughAdjacentSequenceError(msg)
if self._snvs:
real_start = snv_start - len(first_segment)
close_snvs = self._snvs.fetch(chrom.name,
start=real_start,
end=snv_start)
first_segment = _replace_snvs_with_iupac(first_segment,
close_snvs,
seq_offset=real_start)
snv_segment = _build_snv_section(snv)
second_segment = unicode(chrom_seq[snv_end:end])
if len(second_segment) < min_len:
msg = "Not enough sequence in 5'. ID: %s, POS: %d, CHROM: %s"
msg %= (snv.ID, snv.POS, snv.CHROM)
raise self.NotEnoughAdjacentSequenceError(msg)
if self._snvs:
real_end = snv_end + len(second_segment)
close_snvs = self._snvs.fetch(chrom.name,
start=snv_end,
end=real_end)
second_segment = _replace_snvs_with_iupac(second_segment,
close_snvs,
seq_offset=snv_end)
out_fhand = self._out_fhand
sep = self._sep
out_fhand.write(unicode(snv.CHROM))
out_fhand.write(sep)
out_fhand.write(unicode(snv.POS))
out_fhand.write(sep)
snp_id = snv.ID
if snp_id is None:
snp_id = u'.'
out_fhand.write(snp_id)
out_fhand.write(sep)
out_fhand.write(first_segment)
out_fhand.write(snv_segment)
out_fhand.write(second_segment)
out_fhand.write(u'\n')
def flush(self):
self._out_fhand.flush()
def close(self):
self._out_fhand.close()
class IlluminaWriter(object):
'''It writes the SNPs in Illumina format
ref_fpath should be in fasta format and it has to have a name attribute.
min_maf controls the SNPs reported in the adjacent segments as IUPAC codes.
'''
# TODO add extra error classes
# TODO include the error classes inside this class to easy access
class NotEnoughAdjacentSequenceError(Exception):
pass
def __init__(self, ref_fpath, out_fhand, length=60, vcf_fpath=None,
min_length=None):
''''It inits.
The vcf will be used to replace in the reference sequence the SNPs
around the SNP of interest with IUPAC codes
'''
self._sep = u'\t'
self._len = length
if min_length is None:
min_length = length
if min_length > length:
msg = 'Minimum length must be smaller than required length'
raise ValueError(msg)
self._min_len = min_length
self._ref_seqs = seq_index(ref_fpath, format='fasta')
if vcf_fpath:
self._snvs = Reader(filename=vcf_fpath)
else:
self._snvs = None
self._out_fhand = out_fhand
out_fhand.write(u'CHROM\tPOS\tID\tseq\n')
self._prev_chrom = None
def write(self, snv):
chrom_name = snv.CHROM
prev_chrom = self._prev_chrom
if prev_chrom is None or prev_chrom.name != chrom_name:
chrom = self._ref_seqs[chrom_name]
self._prev_chrom = chrom
else:
chrom = prev_chrom
length = self._len
min_len = self._min_len
snv_start = snv.start # 0 based
snv_end = snv.end # 1 based
desired_start = snv_start - length # desired segment start
end = snv_end + length # desired segment end
chrom_seq = chrom.seq
first_segment = unicode(chrom_seq[desired_start:snv_start])
if len(first_segment) < min_len:
msg = "Not enough sequence in 3'. ID: %s, POS: %d, CHROM: %s"
msg %= (snv.ID, snv.POS, snv.CHROM)
raise self.NotEnoughAdjacentSequenceError(msg)
if self._snvs:
real_start = snv_start - len(first_segment)
close_snvs = self._snvs.fetch(chrom.name, start=real_start,
end=snv_start)
first_segment = _replace_snvs_with_iupac(first_segment, close_snvs,
seq_offset=real_start)
snv_segment = _build_snv_section(snv)
second_segment = unicode(chrom_seq[snv_end:end])
if len(second_segment) < min_len:
msg = "Not enough sequence in 5'. ID: %s, POS: %d, CHROM: %s"
msg %= (snv.ID, snv.POS, snv.CHROM)
raise self.NotEnoughAdjacentSequenceError(msg)
if self._snvs:
real_end = snv_end + len(second_segment)
close_snvs = self._snvs.fetch(chrom.name, start=snv_end,
end=real_end)
second_segment = _replace_snvs_with_iupac(second_segment,
close_snvs,
seq_offset=snv_end)
out_fhand = self._out_fhand
sep = self._sep
out_fhand.write(unicode(snv.CHROM))
out_fhand.write(sep)
out_fhand.write(unicode(snv.POS))
out_fhand.write(sep)
snp_id = snv.ID
if snp_id is None:
snp_id = u'.'
out_fhand.write(snp_id)
out_fhand.write(sep)
out_fhand.write(first_segment)
out_fhand.write(snv_segment)
out_fhand.write(second_segment)
out_fhand.write(u'\n')
def flush(self):
self._out_fhand.flush()
def close(self):
self._out_fhand.close()