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