dinuc_shuffling_generator.py

################################################################################
# Module allowing the generation of sequences by using a di-nucleotide
# shuffling of the given sequences
################################################################################

from altschulEriksonDinuclShuffle import dinuclShuffle
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
import re
from utils import GC, split_seq


def generate_sequences(seqs, nfold):
    bg_gc_list = []
    bg_lengths = []
    for record in seqs:
        seq = record.seq.__str__()
        for n in range(0, nfold):
            new_sequence = ""
            for sequence in split_seq(seq):
                if re.match("N", sequence):
                    new_sequence += sequence
                elif sequence:
                    new_sequence += dinuclShuffle(sequence)
            new_seq = SeqRecord(Seq(new_sequence, generic_dna),
                                id="background_seq_for_{0:s}".format(record.name),
                                description="")
            print(new_seq.format("fasta"), end="")
            bg_gc_list.append(GC(new_sequence))
            bg_lengths.append(len(new_sequence))
    return bg_gc_list, bg_lengths