adding kegalign (#26)

tools/kegalign/.shed.yml

@@ -0,0 +1,12 @@
+categories:
+- Next Gen Mappers
+description: A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.
+homepage_url: https://github.com/galaxyproject/KegAlign
+long_description: |
+  KegAlign is a scalable, GPU-accelerated system for computing pairwise
+  WGA. KegAlign is based on the standard seed-filter-extend heuristic,
+  in which the filtering stage dominates the runtime.
+name: kegalign
+owner: richard-burhans
+remote_repository_url: https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign
+type: unrestricted

tools/kegalign/diagonal_partition.py

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+#!/usr/bin/env python
+
+
+"""
+Diagonal partitioning for segment files output by KegAlign.
+
+Usage:
+diagonal_partition.py <max-segments> <lastz-command>
+
+set <max-segments> = 0 to skip partitioning, -1 to estimate best parameter
+"""
+
+import collections
+import os
+import statistics
+import sys
+import typing
+
+
+def chunks(lst: tuple[str, ...], n: int) -> typing.Iterator[tuple[str, ...]]:
+    """Yield successive n-sized chunks from list."""
+    for i in range(0, len(lst), n):
+        yield lst[i:i + n]
+
+
+if __name__ == "__main__":
+    # TODO: make these optional user defined parameters
+
+    # deletes original segment file after splitting
+    DELETE_AFTER_CHUNKING = True
+
+    # don't partition segment files with line count below this value
+    MIN_CHUNK_SIZE = 5000
+
+    # only used when segment size is being estimated
+    MAX_CHUNK_SIZE = 50000
+
+    # include chosen split size in file name
+    DEBUG = False
+
+    # first parameter contains chunk size
+    chunk_size = int(sys.argv[1])
+    params = sys.argv[2:]
+
+    # don't do anything if 0 chunk size
+    if chunk_size == 0:
+        print(" ".join(params), flush=True)
+        sys.exit(0)
+
+    # Parsing command output from KegAlign
+    segment_key = "--segments="
+    segment_index = None
+    input_file = None
+
+    for index, value in enumerate(params):
+        if value[:len(segment_key)] == segment_key:
+            segment_index = index
+            input_file = value[len(segment_key):]
+            break
+
+    if segment_index is None:
+        sys.exit(f"Error: could not get segment key {segment_key} from parameters {params}")
+
+    if input_file is None:
+        sys.exit(f"Error: could not get segment file from parameters {params}")
+
+    if not os.path.isfile(input_file):
+        sys.exit(f"Error: File {input_file} does not exist")
+
+    # each char is 1 byte
+    line_size = None
+    file_size = os.path.getsize(input_file)
+    with open(input_file, "r") as f:
+        # add 1 for newline
+        line_size = len(f.readline())
+
+    estimated_lines = file_size // line_size
+
+    # check if chunk size should be estimated
+    if chunk_size < 0:
+        # optimization, do not need to get each file size in this case
+        if estimated_lines < MIN_CHUNK_SIZE:
+            print(" ".join(params), flush=True)
+            sys.exit(0)
+
+        # get size of each segment assuming DELETE_AFTER_CHUNKING == True
+        # takes into account already split segments
+        files = [i for i in os.listdir(".") if i.endswith(".segments")]
+
+        if len(files) < 2:
+            # if not enough segment files for estimation, use MAX_CHUNK_SIZE
+            chunk_size = MAX_CHUNK_SIZE
+        else:
+            fdict: typing.DefaultDict[str, int] = collections.defaultdict(int)
+            for filename in files:
+                size = os.path.getsize(filename)
+                f_ = filename.split(".split", 1)[0]
+                fdict[f_] += size
+
+            if len(fdict) < 7:
+                # outliers can heavily skew prediction if <7 data points
+                # to be safe, use 50% quantile
+                chunk_size = int(statistics.quantiles(fdict.values())[1] // line_size)
+            else:
+                # otherwise use 75% quantile
+                chunk_size = int(statistics.quantiles(fdict.values())[-1] // line_size)
+            # if not enough data points, there is a chance of getting unlucky
+            # minimize worst case by using MAX_CHUNK_SIZE
+
+            chunk_size = min(chunk_size, MAX_CHUNK_SIZE)
+
+    # no need to sort if number of lines <= chunk_size
+    if (estimated_lines <= chunk_size):
+        print(" ".join(params), flush=True)
+        sys.exit(0)
+
+    # Find rest of relevant parameters
+    output_key = "--output="
+    output_index = None
+    output_alignment_file = None
+    output_alignment_file_base = None
+    output_format = None
+
+    strand_key = "--strand="
+    strand_index = None
+    for index, value in enumerate(params):
+        if value[:len(output_key)] == output_key:
+            output_index = index
+            output_alignment_file = value[len(output_key):]
+            output_alignment_file_base, output_format = output_alignment_file.rsplit(".", 1)
+
+        if value[:len(strand_key)] == strand_key:
+            strand_index = index
+
+    if output_alignment_file_base is None:
+        sys.exit(f"Error: could not get output alignment file base from parameters {params}")
+
+    if output_format is None:
+        sys.exit(f"Error: could not get output format from parameters {params}")
+
+    if output_index is None:
+        sys.exit(f"Error: could not get output key {output_key} from parameters {params}")
+
+    if strand_index is None:
+        sys.exit(f"Error: could not get strand key {strand_key} from parameters {params}")
+
+    # error file is at very end
+    err_index = -1
+    err_name_base = params[-1].split(".err", 1)[0]
+
+    # dict of list of tuple (x, y, str)
+    data: dict[tuple[str, str], list[tuple[int, int, str]]] = {}
+
+    direction = None
+    if "plus" in params[strand_index]:
+        direction = "f"
+    elif "minus" in params[strand_index]:
+        direction = "r"
+    else:
+        sys.exit(f"Error: could not figure out direction from strand value {params[strand_index]}")
+
+    for line in open(input_file, "r"):
+        if line == "":
+            continue
+        seq1_name, seq1_start, seq1_end, seq2_name, seq2_start, seq2_end, _dir, score = line.split()
+        # data.append((int(seq1_start), int(seq2_start), line))
+        half_dist = int((int(seq1_end) - int(seq1_start)) // 2)
+        assert int(seq1_end) > int(seq1_start)
+        assert int(seq2_end) > int(seq2_start)
+        seq1_mid = int(seq1_start) + half_dist
+        seq2_mid = int(seq2_start) + half_dist
+        data.setdefault((seq1_name, seq2_name), []).append((seq1_mid, seq2_mid, line))
+
+    # If there are chromosome pairs with segment count <= chunk_size
+    # then no need to sort and split these pairs into separate files.
+    # It is better to keep these pairs in a single segment file.
+
+    # pairs that have count <= chunk_size. these will not be sorted
+    skip_pairs = []
+
+    # save query key order
+    # for lastz segment files: 'Query sequence names must appear in the same
+    # order as they do in the query file'
+
+    # NOTE: assuming data.keys() preserves order of keys. Requires Python 3.7+
+
+    query_key_order = list(dict.fromkeys([i[1] for i in data.keys()]))
+
+    if len(data.keys()) > 1:
+        for pair in data.keys():
+            if len(data[pair]) <= chunk_size:
+                skip_pairs.append(pair)
+
+    # sorting for forward segments
+    if direction == "r":
+        for pair in data.keys():
+            if pair not in skip_pairs:
+                data[pair] = sorted(data[pair], key=lambda coord: (coord[1] - coord[0], coord[0]))
+
+    # sorting for reverse segments
+    elif direction == "f":
+        for pair in data.keys():
+            if pair not in skip_pairs:
+                data[pair] = sorted(data[pair], key=lambda coord: (coord[1] + coord[0], coord[0]))
+    else:
+        sys.exit(f"INVALID DIRECTION VALUE: {direction}")
+
+    # Writing file in chunks
+    ctr = 0
+    # [i for i in data_keys if i not in set(skip_pairs)]:
+    for pair in (data.keys() - skip_pairs):
+        for chunk in chunks(list(zip(*data[pair]))[2], chunk_size):
+            ctr += 1
+            name_addition = f".split{ctr}"
+
+            if DEBUG:
+                name_addition = f".{chunk_size}{name_addition}"
+
+            fname = input_file.split(".segments", 1)[0] + name_addition + ".segments"
+
+            assert len(chunk) != 0
+            with open(fname, "w") as f:
+                f.writelines(chunk)
+            # update segment file in command
+            params[segment_index] = segment_key + fname
+            # update output file in command
+            params[output_index] = output_key + output_alignment_file_base + name_addition + "." + output_format
+            # update error file in command
+            params[-1] = err_name_base + name_addition + ".err"
+            print(" ".join(params), flush=True)
+
+    # writing unsorted skipped pairs
+    if len(skip_pairs) > 0:
+        # list of tuples of (pair length, pair)
+        skip_pairs_with_len = sorted([(len(data[p]), p) for p in skip_pairs])
+        # NOTE: This sorting can violate lastz query key order requirement, this is fixed later
+
+        # used for sorting
+        query_key_order_table = {item: idx for idx, item in enumerate(query_key_order)}
+
+        # list of list of pair names
+        aggregated_skip_pairs: list[list[tuple[str, str]]] = []
+        current_count = 0
+        aggregated_skip_pairs.append([])
+        for count, pair in skip_pairs_with_len:
+            if current_count + count <= chunk_size:
+                current_count += count
+                aggregated_skip_pairs[-1].append(pair)
+            else:
+                aggregated_skip_pairs.append([])
+                current_count = count
+                aggregated_skip_pairs[-1].append(pair)
+
+        for aggregate in aggregated_skip_pairs:
+            ctr += 1
+            name_addition = f".split{ctr}"
+
+            if DEBUG:
+                name_addition = f".{chunk_size}{name_addition}"
+
+            fname = input_file.split(".segments", 1)[0] + name_addition + ".segments"
+
+            with open(fname, "w") as f:
+                # fix possible lastz query key order violations
+                # p[1] is query key
+                for pair in sorted(aggregate, key=lambda p: query_key_order_table[p[1]]):
+                    chunk = list(zip(*data[pair]))[2]
+                    f.writelines(chunk)
+            # update segment file in command
+            params[segment_index] = segment_key + fname
+            # update output file in command
+            params[output_index] = output_key + output_alignment_file_base + name_addition + "." + output_format
+            # update error file in command
+            params[-1] = err_name_base + name_addition + ".err"
+            print(" ".join(params), flush=True)
+
+    if DELETE_AFTER_CHUNKING:
+        os.remove(input_file)

tools/kegalign/gapped_extension_options.xml

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+<macros>
+    <xml name="gapped_extension_options">
+        <section name="gapped_extension_options" expanded="false" title="Gapped Extension Options">
+            <param argument="--ydrop" type="integer" value="9430" label="Y-drop value for gapped extension"/>
+            <param argument="--gappedthresh" type="integer" value="" optional="true" label="Score threshold for gapped alignments"/>
+            <param argument="--notrivial" type="boolean" checked="false" label="Don't output a trivial self-alignment block if the target and query sequences are identical"/>
+        </section>
+    </xml>
+</macros>