diff utils/preprocess.py @ 0:457fd8fd681a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils/preprocess.py	Wed Nov 09 12:19:26 2022 +0000
@@ -0,0 +1,381 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Credits: Grigorii Sukhorukov, Macha Nikolski
+import math
+import os
+import pathlib
+import random
+
+import h5py
+import numpy as np
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from sklearn.utils import shuffle
+
+
+def reverse_complement(fragment):
+    """
+    provides reverse complement to sequences
+    Input:
+    sequences - list with SeqRecord sequences in fasta format
+    Output:
+    complementary_sequences -
+    list with SeqRecord complementary sequences in fasta format
+    """
+    # complementary_sequences = []
+    # for sequence in sequences:
+    #     complementary_sequence = SeqRecord(
+    #         seq=Seq(sequence.seq).reverse_complement(),
+    #         id=sequence.id + "_reverse_complement",
+    #     )
+    #     complementary_sequences.append(complementary_sequence)
+    fragment = fragment[::-1].translate(str.maketrans('ACGT', 'TGCA'))
+    return fragment
+
+
+def introduce_mutations(seqs, mut_rate, rs=None):
+    """
+    Function that mutates sequences in the entering fasta file
+    A proportion of nucleotides are changed to other nucleotide
+    Not yet taking account of mutation for gaps
+    mut_rate - proportion from 0.0 to 1.0, float
+    """
+    random.seed(a=rs)
+    assert 0.0 <= mut_rate <= 1.0
+    mutated_seqs = []
+    for seq in seqs:
+        mut_seq = list(str(seq.seq))
+        l_ = len(mut_seq)
+        mutated_sites_i = random.sample(range(l_), int(mut_rate * l_))
+        for mut_site_i in mutated_sites_i:
+            mut_site = mut_seq[mut_site_i]
+            mutations = ["A", "C", "T", "G"]
+            if mut_site in mutations:
+                mutations.remove(mut_site)
+                mut_seq[mut_site_i] = random.sample(mutations, 1)[0]
+        mutated_seq = SeqRecord(
+            seq=Seq("".join(mut_seq)),
+            id=seq.id + f"mut_{mut_rate}",
+            name="",
+            description="",
+        )
+        mutated_seqs.append(mutated_seq)
+    return mutated_seqs
+
+
+def separate_by_length(length_, seq_list, fold=None,):
+    # TODO: add docs
+    included = []
+    to_process = []
+    excluded = 0
+    for seq_ in seq_list:
+        l_ = len(seq_.seq)
+        if l_ >= length_:
+            if fold is None:
+                included.append(seq_)
+            elif l_ < length_ * fold:
+                included.append(seq_)
+            else:
+                to_process.append(seq_)
+        else:
+            excluded += 1
+    print(f"A total of {excluded} sequences was excluded due to being smaller than {length_}")
+    return included, to_process
+
+
+def chunks(lst, n):
+    """Yield successive n-sized chunks from lst.
+    https://stackoverflow.com/questions/312443/how-do-you-split-a-list-into-evenly-sized-chunks"""
+    for i in range(0, len(lst), n):
+        yield lst[i:i + n]
+
+
+def correct(frag):
+    """
+    leaves only unambiguous DNA code (ACTG-)
+    Input:
+    frag - string of nucleotides
+    Output:
+    pr_frag - corrected string of nucleotides
+    """
+    pr_frag = frag.upper()
+    pr_frag_s = set(pr_frag)
+    if pr_frag_s != {"A", "C", "G", "T", "-"}:
+        for letter in pr_frag_s - {"A", "C", "G", "T", "-"}:
+            pr_frag = pr_frag.replace(letter, "-")
+    return pr_frag
+
+
+def fragmenting(sequences, sl_wind_size, max_gap=0.05, sl_wind_step=None):
+    """
+    slices sequences in fragments by sliding window
+    based on its size and step.
+    last fragment is padded by '-'
+    fragments have ambiguous bases replaced by '-'
+    fragments with many '-' are discarded
+    Input:
+    sequences - list with SeqRecord sequences in fasta format
+    max_gap - max allowed proportion of '-'
+    sl_wind_size - sliding window step
+    sl_wind_step - sliding window step, by default equals
+    sliding window size (None is replaced by it)
+    Output:
+    fragments - list with sequence fragments
+    """
+    if sl_wind_step is None:
+        sl_wind_step = sl_wind_size
+    fragments = []
+    fragments_rc = []
+    out_sequences = []
+    for sequence in sequences:
+        seq = str(sequence.seq)
+        n_fragments = 1 + max(0, math.ceil((len(seq) - sl_wind_size) / sl_wind_step))
+        for n in range(n_fragments):
+            if n + 1 != n_fragments:
+                frag = seq[n * sl_wind_step: n * sl_wind_step + sl_wind_size]
+            elif n_fragments == 1:
+                # padding the shorter fragment to sl_wind_size
+                frag_short = seq[n * sl_wind_step: n * sl_wind_step + sl_wind_size]
+                frag = frag_short + (sl_wind_size - len(frag_short)) * "-"
+            else:
+                frag = seq[(len(seq) - sl_wind_size):]
+            # replace ambiguous characters
+            frag = correct(frag)
+            assert len(frag) == sl_wind_size, f"{len(frag)} vs {sl_wind_size}"
+            # skipping sequences with many gaps
+            if frag.count("-") / sl_wind_size <= max_gap:
+                fragments.append(frag)
+                # generating reverse complement
+                fragments_rc.append(reverse_complement(frag))
+                fr_seq = SeqRecord(
+                    seq=Seq(frag),
+                    id=f"{sequence.id}_{n*sl_wind_step}_{sl_wind_size}",
+                    name="",
+                    description="",
+                )
+                out_sequences.append(fr_seq)
+    return fragments, fragments_rc, out_sequences
+
+
+def label_fasta_fragments(sequences, label):
+    """
+    Provides labels to generated fragments stored in fasta
+    Input:
+    sequences - list with SeqRecord sequences
+    label - type of label (bacteria, virus, plant)
+    Output:
+    labeled_fragments - list with labeled SeqRecord sequences
+    """
+    assert label in ["virus", "plant", "bacteria"]
+    labeled_fragments = []
+    for sequence in sequences:
+        sequence.id = sequence.id + f"_{label}"
+        labeled_fragments.append(sequence)
+    return labeled_fragments
+
+
+def one_hot_encode(fragments):
+    """
+    produces one-hot matrices from fragments and labels
+    '-' is given all zeros
+    Input:
+    fragments - list with sequence fragments
+    label - type of label (int <= depth)
+    label_depth - number of possible labels
+    Output:
+    encoded_fragments - list with one-hot encoded fragments
+    labels - list with one-hot encoded labels
+    """
+    import tensorflow as tf
+    encoded_fragments = []
+    map_dict = {"A": 0, "C": 1, "G": 2, "T": 3, "-": -1}
+    for frag in fragments:
+        frag_array = np.array(list(frag))
+        integer_encoded = np.int8(np.vectorize(map_dict.get)(frag_array))
+        one_hot_encoded = tf.one_hot(integer_encoded, depth=4, dtype=tf.int8).numpy()
+        encoded_fragments.append(one_hot_encoded)
+    encoded_fragments = np.stack(encoded_fragments)
+    return encoded_fragments
+
+
+def prepare_labels(fragments, label, label_depth):
+    """
+    produces one-hot labels
+    '-' is given all zeros
+    Input:
+    fragments - list with sequence fragments
+    label - type of label (int <= depth)
+    label_depth - number of possible labels
+    Output:
+    labels - list with one-hot encoded labels
+    """
+    import tensorflow as tf
+    n_fragments = len(fragments)
+    labels = np.int8(np.full(n_fragments, label))
+    labels = tf.one_hot(labels, depth=label_depth).numpy()
+    return labels
+
+
+# TODO: write docs for functions
+def calculate_total_length(seq_path):
+    """
+    Calculate total length of the sequences in the fasta file.
+    Needed for weighted sampling
+    Input:
+    seq_path - path to the file with sequences
+    Output:
+    seq_length - total length of all sequences in the file
+    """
+    seqs = list(SeqIO.parse(seq_path, "fasta"))
+    seq_length = 0
+    for seq in seqs:
+        seq_length += len(seq.seq)
+    return seq_length
+
+
+def prepare_seq_lists(in_paths, n_fragments, weights=None,):
+    """
+    selects files with sequences based on extension
+    and calculates number of fragments to be sampled
+    Input:
+    in_paths - list of paths to folder with sequence files. Can be a string also a string
+    n_fragments - number of fragments to be sampled
+    weights - upsampling of fragments. fractions should sum to one
+    Output:
+    seqs_list - list with path to files with sequences
+    n_fragments_list - number of fragments to be sampled
+    """
+    # case when we recieve a single sequence file
+    if type(in_paths) is str and in_paths.endswith(('.fna', '.fasta')):
+        return [[in_paths, n_fragments]]
+    else:
+        # transform string to list
+        if type(in_paths) is str or type(in_paths) is pathlib.PosixPath:
+            in_paths = [in_paths]
+
+        if weights:
+            assert len(weights) == len(in_paths)
+            assert 1.01 > round(sum(weights), 2) > 0.99
+        else:
+            l_ = len(in_paths)
+            weights = [1 / l_] * l_
+        n_fragments_list_all = []
+        seqs_list_all = []
+        for in_paths, w_ in zip(in_paths, weights):
+            seqs_list = []
+            seq_length_list = []
+            total_length = 0
+            for file in os.listdir(in_paths):
+                if file.endswith("fna") or file.endswith("fasta"):
+                    seq_path = (os.path.join(in_paths, file))
+                    seqs_length = calculate_total_length(seq_path)
+                    seqs_list.append(seq_path)
+                    seq_length_list.append(seqs_length)
+                    total_length += seqs_length
+            # + 1 may lead to a slightly bigger number than desired
+            n_fragments_list = [((seq_length / total_length) * n_fragments * w_ + 1) for seq_length in seq_length_list]
+            n_fragments_list_all.extend(n_fragments_list)
+            seqs_list_all.extend(seqs_list)
+        print("list calculation done")
+        return list(zip(seqs_list_all, n_fragments_list_all))
+
+
+def sample_fragments(seq_container, length, random_seed=1, limit=None, max_gap=0.05, sl_wind_step=None):
+    """
+    Randomly samples fragments from sequences in the list.
+    Input:
+    seq_container - list with each entry containing path to sequence,
+    and n samples from this sequence.
+    length - desired length of sampled fragments
+    Output:
+    fragments - list with sequence fragments
+    """
+    random.seed(a=random_seed)
+    total_fragments = []
+    total_fragments_rc = []
+    total_seqs = []
+    for entry in seq_container:
+        seq = list(SeqIO.parse(entry[0], "fasta"))
+        n_fragments = entry[1]
+        seqs = []
+        fragments = []
+        fragments_rc = []
+        counter_1 = 0
+        counter_2 = 0
+        while counter_1 < n_fragments:
+            # select chromosomes if there are any
+            fragment_full = random.choice(seq)
+            r_end = len(fragment_full.seq) - length
+            try:
+                r_start = random.randrange(r_end)
+                fragment = SeqRecord(
+                    seq=fragment_full.seq[r_start:(r_start + length)],
+                    id=f"{fragment_full.id}_{length}_{r_start}",
+                    name="",
+                    description="",
+                )
+                temp_, temp_rc, _ = fragmenting([fragment], length, max_gap, sl_wind_step=sl_wind_step)
+                if temp_ and temp_rc:
+                    seqs.append(fragment)
+                    fragments.extend(temp_)
+                    fragments_rc.extend(temp_rc)
+                    counter_1 += 1
+            except ValueError:
+                # print(f"{fragment_full.id} has length {len(fragment_full.seq)} and is too short to be sampled")
+                pass
+            counter_2 += 1
+            if limit:
+                assert counter_2 <= limit * n_fragments, f"While cycle iterated more than {limit}, data is ambiguous." \
+                                                         f" Only {len(fragments)} fragments were sampled out of {n_fragments}"
+        total_fragments.extend(fragments)
+        total_fragments_rc.extend(fragments_rc)
+        total_seqs.extend(seqs)
+        # print("sequence sampling done")
+    return total_fragments, total_fragments_rc, total_seqs
+
+
+def prepare_ds_fragmenting(in_seq, label, label_int, fragment_length, sl_wind_step, max_gap=0.05, n_cpus=1):
+    if sl_wind_step is None:
+        sl_wind_step = int(fragment_length / 2)
+    # generating viral fragments and labels
+    seqs = list(SeqIO.parse(in_seq, "fasta"))
+    frags, frags_rc, seqs_ = fragmenting(seqs, fragment_length, max_gap=max_gap, sl_wind_step=sl_wind_step)
+    encoded = one_hot_encode(frags)
+    encoded_rc = one_hot_encode(frags_rc)
+    labs = prepare_labels(frags, label=label_int, label_depth=3)
+    seqs_ = label_fasta_fragments(seqs_, label=label)
+    # subsetting to unique fragments
+    u_encoded, indices = np.unique(encoded, axis=0, return_index=True)
+    u_encoded_rc = encoded_rc[indices]
+    u_labs = labs[indices]
+    u_seqs = [seqs_[i] for i in indices]
+    assert (np.shape(u_encoded)[0] == np.shape(u_encoded_rc)[0])
+    print(f"Encoding {label} sequences finished")
+    # print(f"{np.shape(u_encoded)[0]} forward fragments generated")
+    n_frags = np.shape(u_encoded)[0]
+    return u_encoded, u_encoded_rc, u_labs, u_seqs, n_frags
+
+
+def prepare_ds_sampling(in_seqs, fragment_length, n_frags, label, label_int, random_seed, n_cpus=1, limit=100):
+    # generating plant fragments and labels
+    seqs_list = prepare_seq_lists(in_seqs, n_frags)
+    frags, frags_rc, seqs_ = sample_fragments.remote(seqs_list, fragment_length, random_seed, limit=limit, max_gap=0.05)
+    frags, frags_rc, seqs_ = shuffle(frags, frags_rc, seqs_, random_state=random_seed, n_samples=int(n_frags))
+    encoded = one_hot_encode(frags)
+    encoded_rc = one_hot_encode(frags_rc)
+    labs = prepare_labels(frags, label=label_int, label_depth=3)
+    seqs_ = label_fasta_fragments(seqs_, label=label)
+    assert (np.shape(encoded)[0] == np.shape(encoded_rc)[0])
+    print(f"Encoding {label} sequences finished")
+    # print(f"{np.shape(encoded)[0]} forward fragments generated")
+    return encoded, encoded_rc, labs, seqs_, n_frags
+
+
+def storing_encoded(encoded, encoded_rc, labs, out_path, ):
+    f = h5py.File(out_path, "w")
+    f.create_dataset("fragments", data=encoded)
+    f.create_dataset("fragments_rc", data=encoded_rc)
+    f.create_dataset("labels", data=labs)
+    f.close()
+    print(f"encoded fragments and labels stored in {out_path}")