diff scripts/ReMatCh/modules/download.py @ 0:c6bab5103a14 draft

"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/modules/download.py	Mon Mar 21 15:23:09 2022 +0000
@@ -0,0 +1,599 @@
+import os.path
+import multiprocessing
+import sys
+import functools
+import time
+import subprocess
+
+try:
+    import modules.utils as utils
+except ImportError:
+    from ReMatCh.modules import utils as utils
+
+
+def get_read_run_info(ena_id):
+    import urllib.request
+
+    url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=' + ena_id + '&result=read_run'
+
+    read_run_info = None
+    try:
+        url = urllib.request.urlopen(url)
+        read_run_info = url.read().decode("utf8").splitlines()
+        if len(read_run_info) <= 1:
+            read_run_info = None
+    except Exception as error:
+        print(error)
+
+    return read_run_info
+
+
+def get_download_information(read_run_info):
+    header_line = read_run_info[0].split('\t')
+    info_line = read_run_info[1].split('\t')
+
+    download_information = {'fastq': None, 'submitted': None, 'cram_index': None}
+    download_types = ['aspera', 'ftp']
+
+    for i in range(0, len(header_line)):
+        header = header_line[i].lower().rsplit('_', 1)
+        if header[0] in list(download_information.keys()):
+            if header[1] in download_types:
+                if len(info_line[i]) > 0:
+                    files_path = info_line[i].split(';')
+                    if len(files_path) > 2:
+                        print('WARNING: Were found more files than expected in'
+                              ' {download_information}-{download_types} download'
+                              ' links!'.format(download_information=header[0], download_types=header[1]))
+                    if download_information[header[0]] is None:
+                        download_information[header[0]] = {}
+                    download_information[header[0]][header[1]] = files_path
+
+    return download_information
+
+
+def get_sequencing_information(read_run_info):
+    header_line = read_run_info[0].split('\t')
+    info_line = read_run_info[1].split('\t')
+
+    sequencing_information = {'run_accession': None, 'instrument_platform': None, 'instrument_model': None,
+                              'library_layout': None, 'library_source': None, 'extra_run_accession': None,
+                              'nominal_length': None, 'read_count': None, 'base_count': None,
+                              'date_download': time.strftime("%Y-%m-%d")}
+
+    for i in range(0, len(header_line)):
+        header = header_line[i].lower()
+        if header in list(sequencing_information.keys()):
+            if len(info_line[i]) > 0:
+                sequencing_information[header] = info_line[i]
+
+    if len(read_run_info) > 2:
+        extra_run_accession = []
+        for i in range(2, len(read_run_info)):
+            info = read_run_info[i].split('\t')
+            for j in range(0, len(header_line)):
+                header = header_line[j].lower()
+                if header == 'run_accession':
+                    if len(info[j]) > 0:
+                        extra_run_accession.append(info[j])
+        if len(extra_run_accession) >= 1:
+            sequencing_information['extra_run_accession'] = ','.join(extra_run_accession)
+
+    return sequencing_information
+
+
[e-mail]_unhandled_exceptions
+def download_with_aspera(aspera_file_path, aspera_key, outdir, pickle_prefix, sra, ena_id):
+    command = ['ascp', '-QT', '-l', '300m', '', '-i', aspera_key, '', outdir]
+    if not sra:
+        command[4] = '-P33001'
+        command[7] = str('era-fasp@' + aspera_file_path)
+        pickle = pickle_prefix + '.' + aspera_file_path.rsplit('/', 1)[1]
+    else:
+        command[7] = '[e-mail]:/sra/sra-instant/reads/ByRun/sra/{a}/{b}/{c}/{c}.sra'.format(
+            a=ena_id[:3], b=ena_id[:6], c=ena_id)
+        pickle = pickle_prefix + '.' + ena_id
+
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, 3600, True)
+
+    utils.save_variable_to_pickle(run_successfully, outdir, pickle)
+
+
[e-mail]_unhandled_exceptions
+def download_with_wget(ftp_file_path, outdir, pickle_prefix, sra, ena_id):
+    command = ['wget', '--tries=1', '', '-O', '']
+    if not sra:
+        command[2] = ftp_file_path
+        file_download = ftp_file_path.rsplit('/', 1)[1]
+        command[4] = os.path.join(outdir, file_download)
+        pickle = pickle_prefix + '.' + file_download
+    else:
+        command[2] = 'ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/{a}/{b}/{c}/{c}.sra'.format(
+            a=ena_id[:3], b=ena_id[:6], c=ena_id)
+        command[4] = os.path.join(outdir, ena_id + '.sra')
+        pickle = pickle_prefix + '.' + ena_id
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, 3600, True)
+
+    utils.save_variable_to_pickle(run_successfully, outdir, pickle)
+
+
[e-mail]_unhandled_exceptions
+def download_with_sra_prefetch(aspera_key, outdir, pickle_prefix, ena_id):
+    command = ['prefetch', '', ena_id]
+
+    if aspera_key is not None:
+        _, ascp, _ = utils.run_command_popen_communicate(['which', 'ascp'], False, None, False)
+        command[1] = '-a {ascp}|{aspera_key}'.format(ascp=ascp.splitlines()[0], aspera_key=aspera_key)
+
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, 3600, True)
+    if run_successfully:
+        _, prefetch_outdir, _ = utils.run_command_popen_communicate(['echo', '$HOME/ncbi/public/sra'], True, None,
+                                                                    False)
+
+        try:
+            os.rename(os.path.join(prefetch_outdir.splitlines()[0], ena_id + '.sra'),
+                      os.path.join(outdir, ena_id + '.sra'))
+        except OSError as e:
+            print('Found the following error:'
+                  '{}'.format(e))
+
+            from shutil import copy as shutil_copy
+
+            shutil_copy(os.path.join(prefetch_outdir.splitlines()[0], ena_id + '.sra'),
+                        os.path.join(outdir, ena_id + '.sra'))
+            os.remove(os.path.join(prefetch_outdir.splitlines()[0], ena_id + '.sra'))
+
+    utils.save_variable_to_pickle(run_successfully, outdir, pickle_prefix + '.' + ena_id)
+
+
[e-mail]_unhandled_exceptions
+def download_with_curl(ftp_file_path, outdir, pickle_prefix, sra, ena_id):
+    command = ['curl', '--retry', '1', '', '-o', '']
+    if not sra:
+        command[3] = ftp_file_path
+        file_download = ftp_file_path.rsplit('/', 1)[1]
+        command[5] = os.path.join(outdir, file_download)
+        pickle = pickle_prefix + '.' + file_download
+    else:
+        command[3] = 'ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/{a}/{b}/{c}/{c}.sra'.format(
+            a=ena_id[:3], b=ena_id[:6], c=ena_id)
+        command[5] = os.path.join(outdir, ena_id + '.sra')
+        pickle = pickle_prefix + '.' + ena_id
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, 3600, True)
+
+    utils.save_variable_to_pickle(run_successfully, outdir, pickle)
+
+
+def get_pickle_run_successfully(directory, pickle_prefix):
+    run_successfully = True
+    read_pickle = False
+
+    files = find_files(directory, pickle_prefix, '.pkl')
+    if files is not None:
+        for file_found in files:
+            if run_successfully:
+                run_successfully = utils.extract_variable_from_pickle(file_found)
+                read_pickle = True
+
+            os.remove(file_found)
+
+    if not read_pickle:
+        run_successfully = False
+
+    return run_successfully
+
+
+def curl_installed():
+    command = ['which', 'curl']
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, False)
+    return run_successfully
+
+
+def download(download_information_type, aspera_key, outdir, sra, sra_opt, ena_id):
+    pickle_prefix = 'download'
+
+    run_successfully = False
+    download_sra = False
+
+    if not sra:
+        if aspera_key is not None and download_information_type['aspera'] is not None:
+            pool = multiprocessing.Pool(processes=2)
+            for file_download in download_information_type['aspera']:
+                pool.apply_async(download_with_aspera, args=(file_download, aspera_key, outdir, pickle_prefix, sra,
+                                                             ena_id,))
+            pool.close()
+            pool.join()
+            run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+        if not run_successfully and download_information_type['ftp'] is not None:
+            if curl_installed():
+                pool = multiprocessing.Pool(processes=2)
+                for file_download in download_information_type['ftp']:
+                    pool.apply_async(download_with_curl, args=(file_download, outdir, pickle_prefix, sra, ena_id,))
+                pool.close()
+                pool.join()
+                run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+            if not run_successfully:
+                pool = multiprocessing.Pool(processes=2)
+                for file_download in download_information_type['ftp']:
+                    pool.apply_async(download_with_wget, args=(file_download, outdir, pickle_prefix, sra, ena_id,))
+                pool.close()
+                pool.join()
+                run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+
+    if not run_successfully and (sra or sra_opt):
+        if aspera_key is not None:
+            download_with_aspera(None, aspera_key, outdir, pickle_prefix, sra or sra_opt, ena_id)
+            run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+        if not run_successfully:
+            download_with_sra_prefetch(aspera_key, outdir, pickle_prefix, ena_id)
+            run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+            if not run_successfully:
+                if curl_installed():
+                    download_with_curl(None, outdir, pickle_prefix, sra or sra_opt, ena_id)
+                    run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+                if not run_successfully:
+                    download_with_wget(None, outdir, pickle_prefix, sra or sra_opt, ena_id)
+                    run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+
+        if run_successfully:
+            download_sra = True
+
+    return run_successfully, download_sra
+
+
+def download_files(download_information, aspera_key, outdir, download_cram_bam_true, sra, sra_opt, ena_id):
+    run_successfully = False
+    cram_index_run_successfully = False
+    download_sra = False
+
+    if download_information['fastq'] is not None:
+        run_successfully, download_sra = download(download_information['fastq'], aspera_key, outdir, sra, sra_opt,
+                                                  ena_id)
+
+    if not run_successfully:
+        if download_information['submitted'] is not None:
+            if not download_cram_bam_true:
+                cram_bam = False
+                for i in download_information['submitted']:
+                    if download_information['submitted'][i][0].endswith(('.cram', '.bam')):
+                        cram_bam = True
+                        break
+                if not cram_bam:
+                    run_successfully, download_sra = download(download_information['submitted'], aspera_key, outdir,
+                                                              False, False, ena_id)
+
+            elif download_cram_bam_true:
+                run_successfully, download_sra = download(download_information['submitted'], aspera_key, outdir, False,
+                                                          False, ena_id)
+                if run_successfully and download_information['cram_index'] is not None:
+                    cram_index_run_successfully = download(download_information['cram_index'], aspera_key, outdir,
+                                                           False, False, ena_id)
+
+    if not run_successfully and (sra or sra_opt):
+        run_successfully, download_sra = download(download_information['fastq'], aspera_key, outdir, True, sra_opt,
+                                                  ena_id)
+
+    return run_successfully, cram_index_run_successfully, download_sra
+
+
+def sort_alignment(alignment_file, output_file, sort_by_name_true, threads):
+    out_format_string = os.path.splitext(output_file)[1][1:].lower()
+    command = ['samtools', 'sort', '-o', output_file, '-O', out_format_string, '', '-@', str(threads), alignment_file]
+    if sort_by_name_true:
+        command[6] = '-n'
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
+
+    if not run_successfully:
+        output_file = None
+
+    return run_successfully, output_file
+
+
+def alignment_to_fastq(alignment_file, threads, pair_end_type):
+    fastq_basename = os.path.splitext(alignment_file)[0]
+    outfiles = None
+    bam_file = fastq_basename + '.temp.bam'
+    # sort cram
+    run_successfully, bam_file = sort_alignment(alignment_file, bam_file, True, threads)
+    if run_successfully:
+        command = ['samtools', 'fastq', '', bam_file]
+        if pair_end_type.lower() == 'paired':
+            command[2] = '-1 ' + str(fastq_basename + '_1.fq') + ' -2 ' + str(fastq_basename + '_2.fq')
+        elif pair_end_type == 'single':
+            command[2] = '-0 ' + str(fastq_basename + '.fq')
+
+        run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
+        if run_successfully:
+            if pair_end_type.lower() == 'paired':
+                outfiles = [str(fastq_basename + '_1.fq'), str(fastq_basename + '_2.fq')]
+            elif pair_end_type.lower() == 'single':
+                outfiles = [str(fastq_basename + '.fq')]
+
+    if bam_file is not None and os.path.isfile(bam_file):
+        os.remove(bam_file)
+
+    return run_successfully, outfiles
+
+
+def formart_fastq_headers(in_fastq_1, in_fastq_2):
+
+    out_fastq_1 = in_fastq_1 + '.temp'
+    out_fastq_2 = in_fastq_2 + '.temp'
+    writer_in_fastq_1 = open(out_fastq_1, 'wt')
+    writer_in_fastq_2 = open(out_fastq_2, 'wt')
+    outfiles = [out_fastq_1, out_fastq_2]
+    with open(in_fastq_1, 'rtU') as reader_in_fastq_1, open(in_fastq_2, 'rtU') as reader_in_fastq_2:
+        plus_line = True
+        quality_line = True
+        number_reads = 0
+        for in_1, in_2 in zip(reader_in_fastq_1, reader_in_fastq_2):
+            if len(in_1) > 0:
+                in_1 = in_1.splitlines()[0]
+                in_2 = in_2.splitlines()[0]
+                if in_1.startswith('@') and plus_line and quality_line:
+                    if in_1 != in_2:
+                        sys.exit('The PE fastq files are not aligned properly!')
+                    in_1 += '/1' + '\n'
+                    in_2 += '/2' + '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_2)
+                    plus_line = False
+                    quality_line = False
+                elif in_1.startswith('+') and not plus_line:
+                    in_1 += '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_1)
+                    plus_line = True
+                elif plus_line and not quality_line:
+                    in_1 += '\n'
+                    in_2 += '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_2)
+                    writer_in_fastq_1.flush()
+                    writer_in_fastq_2.flush()
+                    number_reads += 1
+                    quality_line = True
+                else:
+                    in_1 += '\n'
+                    in_2 += '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_2)
+    return number_reads, outfiles
+
+
[e-mail]_unhandled_exceptions
+def gzip_files(file_2_compress, pickle_prefix, outdir):
+    if file_2_compress.endswith('.temp'):
+        out_file = os.path.splitext(file_2_compress)[0]
+    else:
+        out_file = file_2_compress
+
+    command = ['gzip', '--stdout', '--best', file_2_compress, '>', str(out_file + '.gz')]
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, True, None, True)
+    if run_successfully:
+        os.remove(file_2_compress)
+
+    utils.save_variable_to_pickle(run_successfully, outdir,
+                                  str(pickle_prefix + '.' + os.path.basename(file_2_compress)))
+
+
+def find_files(directory, prefix, suffix):
+    list_files_found = []
+    files = [f for f in os.listdir(directory) if not f.startswith('.') and os.path.isfile(os.path.join(directory, f))]
+    for file_found in files:
+        if file_found.startswith(prefix) and file_found.endswith(suffix):
+            file_path = os.path.join(directory, file_found)
+            list_files_found.append(file_path)
+
+    if len(list_files_found) == 0:
+        list_files_found = None
+
+    return list_files_found
+
+
+def compress_files(fastq_files, outdir, threads):
+    pickle_prefix = 'compress'
+    compressed_fastq_files = None
+
+    pool = multiprocessing.Pool(processes=threads)
+    for fastq in fastq_files:
+        pool.apply_async(gzip_files, args=(fastq, pickle_prefix, outdir,))
+    pool.close()
+    pool.join()
+
+    run_successfully = get_pickle_run_successfully(outdir, pickle_prefix)
+    if run_successfully:
+        compressed_fastq_files = find_files(outdir, '', '.gz')
+
+    return run_successfully, compressed_fastq_files
+
+
+def bam_cram_2_fastq(alignment_file, outdir, threads, pair_end_type):
+    run_successfully, fastq_files = alignment_to_fastq(alignment_file, threads, pair_end_type)
+    if run_successfully:
+        if pair_end_type.lower() == 'paired':
+            number_reads, fastq_files = formart_fastq_headers(fastq_files[0], fastq_files[1])
+
+        run_successfully, fastq_files = compress_files(fastq_files, outdir, threads)
+
+    return run_successfully, fastq_files
+
+
+def check_correct_links(download_information):
+    for i in download_information:
+        if download_information[i] is not None:
+            if download_information[i]['aspera'] is not None:
+                for j in range(0, len(download_information[i]['aspera'])):
+                    if download_information[i]['aspera'][j].startswith('fasp.sra.ebi.ac.uk/'):
+                        download_information[i]['aspera'][j] = download_information[i]['aspera'][j].replace(
+                            'fasp.sra.ebi.ac.uk/', 'fasp.sra.ebi.ac.uk:/', 1)
+            if download_information[i]['ftp'] is not None:
+                for j in range(0, len(download_information[i]['ftp'])):
+                    if '#' in download_information[i]['ftp'][j]:
+                        download_information[i]['ftp'][j] = download_information[i]['ftp'][j].replace('#', '%23')
+    return download_information
+
+
+def get_fastq_files(download_dir, cram_index_run_successfully, threads, download_paired_type):
+    run_successfully = False
+    downloaded_files = find_files(download_dir, '', '')
+    if cram_index_run_successfully:
+        cram_file = None
+        for i in downloaded_files:
+            if i.endswith('.cram'):
+                cram_file = i
+        run_successfully, downloaded_files = bam_cram_2_fastq(cram_file, download_dir, threads, download_paired_type)
+    else:
+        if downloaded_files is not None and len(downloaded_files) > 0:
+            run_successfully = True
+
+    return run_successfully, downloaded_files
+
+
+def rename_move_files(list_files, new_name, outdir, download_paired_type):
+    list_new_files = {}
+    run_successfully = False
+
+    for i in range(0, len(list_files)):
+        temp_name = utils.rchop(os.path.basename(list_files[i]), 'astq.gz')
+        if len(temp_name) == len(os.path.basename(list_files[i])):
+            temp_name = utils.rchop(os.path.basename(list_files[i]), 'q.gz')
+        if download_paired_type.lower() == 'paired':
+            if temp_name.endswith(('_R1_001.f', '_1.f')):
+                list_new_files[i] = os.path.join(outdir, new_name + '_1.fq.gz')
+            elif temp_name.endswith(('_R2_001.f', '_2.f')):
+                list_new_files[i] = os.path.join(outdir, new_name + '_2.fq.gz')
+        else:
+            if not temp_name.endswith(('_R1_001.f', '_R2_001.f')):
+                list_new_files[i] = os.path.join(outdir, new_name + '.fq.gz')
+                if temp_name.endswith(('_1.f', '_2.f')):
+                    print('WARNING: possible single-end file conflict with pair-end (' + list_files[i] + ')!')
+
+    if len(list_new_files) == 2 and download_paired_type.lower() == 'paired':
+        run_successfully = True
+    elif len(list_new_files) == 1 and download_paired_type.lower() == 'single':
+        run_successfully = True
+
+    if run_successfully:
+        try:
+            for i in range(0, len(list_files)):
+                if i not in list_new_files:
+                    if os.path.isfile(list_files[i]):
+                        os.remove(list_files[i])
+                else:
+                    os.rename(list_files[i], list_new_files[i])
+            list_new_files = list(list_new_files.values())
+        except Exception as e:
+            print(e)
+            run_successfully = False
+
+    if not run_successfully:
+        list_new_files = None
+
+    return run_successfully, list_new_files
+
+
+# @utils.trace_unhandled_exceptions
+def rename_header_sra(fastq):
+    run_successfully = False
+    try:
+        command = ['gawk', '\'{if(NR%4==1) $0=gensub(/\./, \"/\", 2); print}\'', fastq, '|', 'gzip', '-1', '>',
+                   str(fastq + '.gz')]
+        print('Running: ' + str(' '.join(command)))
+        return_code = subprocess.call(' '.join(command), shell=True)
+        if return_code == 0:
+            run_successfully = True
+        else:
+            print('Something went wrong with command: {command}'.format(command=' '.join(command)))
+    except Exception as e:
+        print(e)
+
+    return run_successfully
+
+
+def sra_2_fastq(download_dir, ena_id):
+    command = ['fastq-dump', '-I', '-O', download_dir, '--split-files', '{download_dir}{ena_id}.sra'.format(
+        download_dir=download_dir, ena_id=ena_id)]
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, 3600, True)
+    if run_successfully:
+        files = [os.path.join(download_dir, f) for f in os.listdir(download_dir)
+                 if not f.startswith('.') and os.path.isfile(os.path.join(download_dir, f)) and f.endswith('.fastq')]
+
+        pool = multiprocessing.Pool(processes=2)
+        results = []
+        p = pool.map_async(rename_header_sra, files, callback=results.extend)
+        p.wait()
+
+        run_successfully = all(results)
+
+    return run_successfully
+
+
+download_timer = functools.partial(utils.timer, name='Download module')
+
+
+@download_timer
+def run_download(ena_id, download_paired_type, aspera_key, outdir, download_cram_bam_true, threads, instrument_platform,
+                 sra, sra_opt):
+    download_dir = os.path.join(outdir, 'download', '')
+    utils.remove_directory(download_dir)
+    os.mkdir(download_dir)
+
+    run_successfully = False
+    downloaded_files = None
+    sequencing_information = {'run_accession': None, 'instrument_platform': None, 'instrument_model': None,
+                              'library_layout': None, 'library_source': None, 'extra_run_accession': None,
+                              'nominal_length': None, 'read_count': None, 'base_count': None,
+                              'date_download': time.strftime("%Y-%m-%d")}
+
+    read_run_info = get_read_run_info(ena_id)
+    if read_run_info is not None:
+        download_information = get_download_information(read_run_info)
+        download_information = check_correct_links(download_information)
+        sequencing_information = get_sequencing_information(read_run_info)
+
+        if instrument_platform.lower() == 'all' or \
+                (sequencing_information['instrument_platform'] is not None and
+                 sequencing_information['instrument_platform'].lower() == instrument_platform.lower()):
+            if download_paired_type.lower() == 'both' or \
+                    (sequencing_information['library_layout'] is not None and
+                     sequencing_information['library_layout'].lower() == download_paired_type.lower()):
+                run_successfully, cram_index_run_successfully, download_sra = download_files(download_information,
+                                                                                             aspera_key, download_dir,
+                                                                                             download_cram_bam_true,
+                                                                                             sra, sra_opt, ena_id)
+                if download_sra:
+                    run_successfully = sra_2_fastq(download_dir, ena_id)
+                if run_successfully:
+                    run_successfully, downloaded_files = get_fastq_files(download_dir, cram_index_run_successfully,
+                                                                         threads,
+                                                                         sequencing_information['library_layout'])
+                if run_successfully and downloaded_files is not None:
+                    run_successfully, downloaded_files = rename_move_files(downloaded_files,
+                                                                           sequencing_information['run_accession'],
+                                                                           outdir,
+                                                                           sequencing_information['library_layout'])
+    else:
+        if sra or sra_opt:
+            run_successfully, cram_index_run_successfully, download_sra = download_files({'fastq': None,
+                                                                                          'submitted': None,
+                                                                                          'cram_index': None},
+                                                                                         aspera_key, download_dir,
+                                                                                         download_cram_bam_true, sra,
+                                                                                         sra_opt, ena_id)
+            if download_sra:
+                run_successfully = sra_2_fastq(download_dir, ena_id)
+            if run_successfully:
+                run_successfully, downloaded_files = get_fastq_files(download_dir, cram_index_run_successfully, threads,
+                                                                     'paired')
+                if not run_successfully:
+                    run_successfully, downloaded_files = get_fastq_files(download_dir, cram_index_run_successfully,
+                                                                         threads, 'single')
+            if run_successfully and downloaded_files is not None:
+                run_successfully, downloaded_files = rename_move_files(downloaded_files, ena_id, outdir, 'paired')
+                if not run_successfully:
+                    run_successfully, downloaded_files = rename_move_files(downloaded_files, ena_id, outdir, 'single')
+
+    utils.remove_directory(download_dir)
+
+    return run_successfully, downloaded_files, sequencing_information