annotate data_manager/data_manager_gatk_picard_index_builder.py @ 7:0f85d523291e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder commit a54e50916ebdb0858b049cdc549a43df801e1a71

#!/usr/bin/env python
# Dave B.
# Uses fasta sorting functions written by Dan Blankenberg.

import json
import optparse
import os
import shutil
import subprocess
import sys
import tempfile

CHUNK_SIZE = 2**20
DEFAULT_DATA_TABLE_NAME = "fasta_indexes"


def get_id_name(params, dbkey, fasta_description=None):
    # TODO: ensure sequence_id is unique and does not already appear in location file
    sequence_id = params['param_dict']['sequence_id']
    if not sequence_id:
        sequence_id = dbkey

    sequence_name = params['param_dict']['sequence_name']
    if not sequence_name:
        sequence_name = fasta_description
        if not sequence_name:
            sequence_name = dbkey
    return sequence_id, sequence_name


def build_picard_index(data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME):
    fasta_base_name = os.path.split(fasta_filename)[-1]
    gatk_sorted_fasta_filename = os.path.join(target_directory, fasta_base_name)
    shutil.copy(fasta_filename, gatk_sorted_fasta_filename)
    _sort_fasta_gatk(gatk_sorted_fasta_filename)
    sam_index_filename = '%s.fai' % gatk_sorted_fasta_filename
    if not os.path.exists(sam_index_filename):
        sam_command = ['samtools', 'faidx', gatk_sorted_fasta_filename]
        _run_command(sam_command, target_directory)
    args = ['java', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id]
    _run_command(args, target_directory)
    data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)


def _run_command(command, target_directory):
    tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-gatk_picard_index_builder-stderr")
    proc = subprocess.Popen(args=command, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())
    return_code = proc.wait()
    if return_code:
        tmp_stderr.flush()
        tmp_stderr.seek(0)
        sys.stderr.write("Error building index:\n")
        while True:
            chunk = tmp_stderr.read(CHUNK_SIZE)
            if not chunk:
                break
            sys.stderr.write(chunk)
        sys.exit(return_code)
    tmp_stderr.close()


def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
    return data_manager_dict


def _move_and_index_fasta_for_sorting(fasta_filename):
    unsorted_filename = tempfile.NamedTemporaryFile().name
    shutil.move(fasta_filename, unsorted_filename)
    fasta_offsets = {}
    with open(unsorted_filename) as unsorted_fh:
        while True:
            offset = unsorted_fh.tell()
            line = unsorted_fh.readline()
            if not line:
                break
            if line.startswith(">"):
                line = line.split(None, 1)[0][1:]
                fasta_offsets[line] = offset
    current_order = [x[1] for x in sorted((x[1], x[0]) for x in fasta_offsets.items())]
    return (unsorted_filename, fasta_offsets, current_order)


def _write_sorted_fasta(sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename):
    with open(unsorted_fasta_filename, 'rb') as unsorted_fh, open(sorted_fasta_filename, 'wb+') as sorted_fh:
        for name in sorted_names:
            offset = fasta_offsets[name]
            unsorted_fh.seek(offset)
            sorted_fh.write(unsorted_fh.readline())
            while True:
                line = unsorted_fh.readline()
                if not line or line.startswith(b">"):
                    break
                sorted_fh.write(line)


def _int_to_roman(integer):
    if not isinstance(integer, int):
        raise TypeError("expected integer, got %s" % type(integer))
    if not 0 < integer < 4000:
        raise ValueError("Argument must be between 1 and 3999, got %s" % str(integer))
    ints = (1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1)
    nums = ('M', 'CM', 'D', 'CD', 'C', 'XC', 'L', 'XL', 'X', 'IX', 'V', 'IV', 'I')
    result = ""
    for i in range(len(ints)):
        count = int(integer / ints[i])
        result += nums[i] * count
        integer -= ints[i] * count
    return result


def _sort_fasta_gatk(fasta_filename):
    (unsorted_filename, fasta_offsets, current_order) = _move_and_index_fasta_for_sorting(fasta_filename)
    sorted_names = list(map(str, range(1, 100))) + list(map(_int_to_roman, range(1, 100))) + ['X', 'Y', 'M']
    # detect if we have chrN, or just N
    has_chr = False
    for chrom in sorted_names:
        if "chr%s" % chrom in current_order:
            has_chr = True
            break

    if has_chr:
        sorted_names = ["chr%s" % x for x in sorted_names]
    else:
        sorted_names.insert(0, "MT")
    sorted_names.extend(["%s_random" % x for x in sorted_names])

    existing_sorted_names = []
    for name in sorted_names:
        # Append each chromosome only once.
        if name in current_order and name not in existing_sorted_names:
            existing_sorted_names.append(name)
    for name in current_order:
        # TODO: confirm that non-canonical names do not need to be sorted specially
        if name not in existing_sorted_names:
            existing_sorted_names.append(name)

    if existing_sorted_names == current_order:
        shutil.move(unsorted_filename, fasta_filename)
    else:
        _write_sorted_fasta(existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename)


def main():
    parser = optparse.OptionParser()
    parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
    parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
    parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
    parser.add_option('-j', '--jar', dest='jar', action='store', type="string", default=None, help='GATK .jar file')
    (options, args) = parser.parse_args()

    filename = args[0]

    with open(filename) as fh:
        params = json.load(fh)
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    data_manager_dict = {}

    if options.fasta_dbkey in [None, '', '?']:
        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (options.fasta_dbkey))

    sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)

    # build the index
    build_picard_index(data_manager_dict,
                       options.fasta_filename,
                       target_directory,
                       options.fasta_dbkey,
                       sequence_id,
                       sequence_name,
                       options.jar,
                       data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME)

    # save info to json file
    with open(filename, 'w') as fh:
        json.dump(data_manager_dict, fh, sort_keys=True)


if __name__ == "__main__":
    main()