def __init__(self, ref_fpath, orf_seq_fpath):
self.orf_suffix = '_orf_seq'
self.ref_index = seq_index(ref_fpath, 'fasta')
self.orf_seq_index = seq_index(orf_seq_fpath, 'fasta')
blossum_path = join(DATA_DIR, 'blossum90.csv')
self.blosum = _parse_blossum_matrix(blossum_path)
self.conf = {}
def __init__(self, ref_fpath, orf_seq_fpath):
self.orf_suffix = '_orf_seq'
self.ref_index = seq_index(ref_fpath, 'fasta')
self.orf_seq_index = seq_index(orf_seq_fpath, 'fasta')
blossum_path = join(DATA_DIR, 'blossum90.csv')
self.blosum = _parse_blossum_matrix(blossum_path)
self.conf = {}
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, 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, ref_fpath, dust_threshold=DEFATULT_DUST_THRESHOLD,
window=DEF_SNP_DUST_WINDOW):
self.threshold = dust_threshold
self.window = window
self.ref_index = seq_index(ref_fpath, 'fasta')
self._last_chrom = None
self._scores = array('f')
def __init__(self, ref_fpath, dust_threshold=DEFATULT_DUST_THRESHOLD,
window=DEF_SNP_DUST_WINDOW):
self.threshold = dust_threshold
self.window = window
self.ref_index = seq_index(ref_fpath, 'fasta')
self._last_chrom = None
self._scores = array('f')
def __init__(self, ref_fpath, orf_seq_fpath):
self.orf_suffix = '_orf_seq'
self.ref_index = seq_index(ref_fpath, 'fasta')
self.orf_seq_index = seq_index(orf_seq_fpath, 'fasta')
self.conf = {}
def __init__(self, all_enzymes, ref_fpath):
self.all_enzymes = all_enzymes
self.ref_index = seq_index(ref_fpath, 'fasta')
self.conf = {'all_enzymes': all_enzymes}
self._last_chrom = None
def __init__(self, ref_fpath, orf_seq_fpath):
self.orf_suffix = '_orf_seq'
self.ref_index = seq_index(ref_fpath, 'fasta')
self.orf_seq_index = seq_index(orf_seq_fpath, 'fasta')
self.conf = {}
def __init__(self, all_enzymes, ref_fpath):
self.all_enzymes = all_enzymes
self.ref_index = seq_index(ref_fpath, 'fasta')
self.conf = {'all_enzymes': all_enzymes}
self._last_chrom = None
