annotate tn93_cluster.py @ 2:eb6f0ec5b95e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit e9f254ea1c6712a96512cae4df91bfec8207a492

import argparse
import json
import os
import shlex
import subprocess
import sys


def cluster_to_fasta(json_file, fasta_file, reference_name=None):
    with open(json_file, "r") as fh:
        cluster_json = json.load(fh)
        with open(fasta_file, "w") as fh2:
            for c in cluster_json:
                if reference_name is not None:
                    if reference_name in c["members"]:
                        cc = c["centroid"].split("\n")
                        cc[0] = ">" + reference_name
                        print("\n".join(cc), file=fh2)
                        continue
                print(c["centroid"], file=fh2)

    return (os.path.getmtime(fasta_file), len(cluster_json))


def run_command(command):
    proc = subprocess.Popen(
        shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE
    )
    stdout, stderr = proc.communicate()
    result = proc.returncode
    if result != 0:
        print(
            "Command `%s` failed with exit code %s\n" % (command, result),
            file=sys.stderr,
        )
        print("--------------------- STDOUT ---------------------")
        print(stdout.decode().replace("\\n", "\n"))
        print("------------------- END STDOUT -------------------")
        print("--------------------- STDERR ---------------------", file=sys.stderr)
        print(stderr.decode().replace("\\n", "\n"), file=sys.stderr)
        print("------------------- END STDERR -------------------", file=sys.stderr)
    return int(result)


def main(arguments):
    threshold = arguments.threshold
    step = threshold * 0.25
    with open(arguments.reference) as fh:
        for line in fh:
            if line[0] == ">":
                _ref_seq_name = line[1:].split(" ")[0].strip()
                break
    while threshold <= 1:
        command = (
            "tn93-cluster -o clusters.json -t %g -a %s -c %s -m json -l %d -g %f %s"
            % (
                threshold,
                arguments.ambigs,
                arguments.cluster_type,
                arguments.overlap,
                arguments.fraction,
                arguments.input,
            )
        )
        return_code = run_command(command)
        if return_code != 0:
            return return_code
        input_stamp, cluster_count = cluster_to_fasta(
            "clusters.json", "clusters.fa", _ref_seq_name
        )
        if cluster_count <= arguments.cluster_count:
            break
        else:
            threshold += step
        print("Found %d clusters at threshold %f" % (cluster_count, threshold))
    return 0


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Combine alignments into a single file, adding a reference sequence as well"
    )
    parser.add_argument("--input", help="Input MSA", required=True, type=str)
    parser.add_argument(
        "--reference", help="Reference sequence", required=True, type=str
    )
    parser.add_argument("--output", help="Input MSA", required=True, type=str)
    parser.add_argument("--threshold", help="Threshold", required=True, type=float)
    parser.add_argument("--ambigs", help="Handle ambigs", required=True, type=str)
    parser.add_argument("--cluster-type", help="Cluster type", required=True, type=str)
    parser.add_argument("--overlap", help="Overlap", required=True, type=int)
    parser.add_argument("--fraction", help="Fraction", required=True, type=float)
    parser.add_argument("--cluster-count", help="Max query", required=True, type=int)
    parser.add_argument(
        "--compressed",
        help="File to write compressed clusters to",
        required=True,
        type=str,
    )
    arguments = parser.parse_args()
    exit(main(arguments))