mononuc_window_shuffling_generator.py

"""
Shuffle input sequences within a sliding window, keeping mononuc compo.

Written by Luis del Peso
Modified by A. Mathelier

"""

from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from utils import GC
import random


def shuffle_window(ss, wl, step):
    """
    Shuffle sequence in the given window.

    Return the shuffled sequence.

    """

    bs = ss[:]
    for i in range(0, len(bs) - 1, step):
        substring = bs[i:(i + wl)]
        bs = ''.join([bs[0:i],
                      ''.join(random.sample(substring, len(substring))),
                      bs[i + wl:]])
    return bs


def generate_sequences(seqs, winlen, step, nfold):
    """
    Shuffle sequences within a sliding window, keeping mononuc compo.

    Return %GC and length distribution of output sequences.

    """

    cpt = 1
    bg_gc_list = []
    bg_lengths = []
    for record in seqs:
        sequence = record.seq.__str__()
        descr = "Background sequence for {0:s}".format(record.name, cpt)
        for _ in range(0, nfold):
            new_sequence = shuffle_window(sequence, winlen, step)
            new_seq = SeqRecord(Seq(new_sequence, generic_dna),
                                id="background_seq_{0:d}".format(cpt),
                                description=descr)
            print new_seq.format("fasta"),
            bg_gc_list.append(GC(new_sequence))
            bg_lengths.append(len(new_sequence))
            cpt += 1
    return bg_gc_list, bg_lengths