Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
annotate data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py @ 8:14eb0fc65c62 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
author | iuc |
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date | Wed, 16 Oct 2019 04:17:00 -0400 |
parents | b1bc53e9bbc5 |
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rev | line source |
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0 | 1 #!/usr/bin/env python |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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2 # Dan Blankenberg |
0 | 3 |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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4 import bz2 |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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5 import gzip |
8
14eb0fc65c62
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
iuc
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6 import json |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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7 import optparse |
0 | 8 import os |
9 import shutil | |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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10 import sys |
0 | 11 import tarfile |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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12 import tempfile |
0 | 13 import zipfile |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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14 from ftplib import FTP |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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15 |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
devteam
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16 try: |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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17 # For Python 3.0 and later |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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18 from io import BytesIO as StringIO |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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19 from io import UnsupportedOperation |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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20 from urllib.request import urlopen |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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21 except ImportError: |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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22 # Fall back to Python 2 imports |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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23 from StringIO import StringIO |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
devteam
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24 from urllib2 import urlopen |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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25 |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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26 UnsupportedOperation = AttributeError |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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27 |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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28 CHUNK_SIZE = 2 ** 20 # 1mb |
0 | 29 |
30 | |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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31 def cleanup_before_exit(tmp_dir): |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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32 if tmp_dir and os.path.exists(tmp_dir): |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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33 shutil.rmtree(tmp_dir) |
0 | 34 |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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35 |
0 | 36 def stop_err(msg): |
37 sys.stderr.write(msg) | |
38 sys.exit(1) | |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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39 |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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40 |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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41 def get_dbkey_dbname_id_name(params, dbkey_description=None): |
0 | 42 dbkey = params['param_dict']['dbkey_source']['dbkey'] |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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43 # TODO: ensure sequence_id is unique and does not already appear in location file |
0 | 44 sequence_id = params['param_dict']['sequence_id'] |
45 if not sequence_id: | |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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46 sequence_id = dbkey # uuid.uuid4() generate and use an uuid instead? |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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47 |
0 | 48 if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new': |
49 dbkey_name = params['param_dict']['dbkey_source']['dbkey_name'] | |
50 if not dbkey_name: | |
51 dbkey_name = dbkey | |
52 else: | |
53 dbkey_name = None | |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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54 |
0 | 55 sequence_name = params['param_dict']['sequence_name'] |
56 if not sequence_name: | |
57 sequence_name = dbkey_description | |
58 if not sequence_name: | |
59 sequence_name = dbkey | |
60 return dbkey, dbkey_name, sequence_id, sequence_name | |
61 | |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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62 |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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63 def _get_files_in_ftp_path(ftp, path): |
0 | 64 path_contents = [] |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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65 ftp.retrlines('MLSD %s' % (path), path_contents.append) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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66 return [line.split(';')[-1].lstrip() for line in path_contents] |
0 | 67 |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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68 |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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69 def _get_stream_readers_for_tar(fh, tmp_dir): |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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70 fasta_tar = tarfile.open(fileobj=fh, mode='r:*') |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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71 return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x] |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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72 |
0 | 73 |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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74 def _get_stream_readers_for_zip(fh, tmp_dir): |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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75 """ |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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76 Unpacks all archived files in a zip file. |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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77 Individual files will be concatenated (in _stream_fasta_to_file) |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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78 """ |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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79 fasta_zip = zipfile.ZipFile(fh, 'r') |
0 | 80 rval = [] |
81 for member in fasta_zip.namelist(): | |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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82 fasta_zip.extract(member, tmp_dir) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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83 rval.append(open(os.path.join(tmp_dir, member), 'rb')) |
0 | 84 return rval |
85 | |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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86 |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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87 def _get_stream_readers_for_gzip(fh, tmp_dir): |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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88 return [gzip.GzipFile(fileobj=fh, mode='rb')] |
0 | 89 |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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90 |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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91 def _get_stream_readers_for_bz2(fh, tmp_dir): |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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92 return [bz2.BZ2File(fh.name, 'rb')] |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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93 |
0 | 94 |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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95 def sort_fasta(fasta_filename, sort_method, params): |
0 | 96 if sort_method is None: |
97 return | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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98 assert sort_method in SORTING_METHODS, ValueError("%s is not a valid sorting option." % sort_method) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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99 return SORTING_METHODS[sort_method](fasta_filename, params) |
0 | 100 |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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101 |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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102 def _move_and_index_fasta_for_sorting(fasta_filename): |
0 | 103 unsorted_filename = tempfile.NamedTemporaryFile().name |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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104 shutil.move(fasta_filename, unsorted_filename) |
0 | 105 fasta_offsets = {} |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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106 unsorted_fh = open(unsorted_filename) |
0 | 107 while True: |
108 offset = unsorted_fh.tell() | |
109 line = unsorted_fh.readline() | |
110 if not line: | |
111 break | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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112 if line.startswith(">"): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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113 line = line.split(None, 1)[0][1:] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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114 fasta_offsets[line] = offset |
0 | 115 unsorted_fh.close() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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116 current_order = [_[1] for _ in sorted((_[1], _[0]) for _ in fasta_offsets.items())] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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117 return (unsorted_filename, fasta_offsets, current_order) |
0 | 118 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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119 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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120 def _write_sorted_fasta(sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename): |
8
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121 with open(unsorted_fasta_filename, 'rb') as unsorted_fh, open(sorted_fasta_filename, 'wb+') as sorted_fh: |
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122 for name in sorted_names: |
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123 offset = fasta_offsets[name] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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124 unsorted_fh.seek(offset) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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125 sorted_fh.write(unsorted_fh.readline()) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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126 while True: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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127 line = unsorted_fh.readline() |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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128 if not line or line.startswith(b">"): |
14eb0fc65c62
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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129 break |
14eb0fc65c62
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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130 sorted_fh.write(line) |
0 | 131 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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132 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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133 def _sort_fasta_as_is(fasta_filename, params): |
0 | 134 return |
135 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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136 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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137 def _sort_fasta_lexicographical(fasta_filename, params): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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138 (unsorted_filename, fasta_offsets, current_order) = _move_and_index_fasta_for_sorting(fasta_filename) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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139 sorted_names = sorted(fasta_offsets.keys()) |
0 | 140 if sorted_names == current_order: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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141 shutil.move(unsorted_filename, fasta_filename) |
0 | 142 else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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143 _write_sorted_fasta(sorted_names, fasta_offsets, fasta_filename, unsorted_filename) |
0 | 144 |
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145 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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146 def _sort_fasta_gatk(fasta_filename, params): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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147 (unsorted_filename, fasta_offsets, current_order) = _move_and_index_fasta_for_sorting(fasta_filename) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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148 sorted_names = list(map(str, range(1, 23))) + ['X', 'Y'] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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149 # detect if we have chrN, or just N |
0 | 150 has_chr = False |
151 for chrom in sorted_names: | |
152 if "chr%s" % chrom in current_order: | |
153 has_chr = True | |
154 break | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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155 |
0 | 156 if has_chr: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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157 sorted_names = ["chr%s" % x for x in sorted_names] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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158 sorted_names.insert(0, "chrM") |
0 | 159 else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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160 sorted_names.insert(0, "MT") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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161 sorted_names.extend("%s_random" % x for x in sorted_names) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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162 |
0 | 163 existing_sorted_names = [] |
164 for name in sorted_names: | |
165 if name in current_order: | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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166 existing_sorted_names.append(name) |
0 | 167 for name in current_order: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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168 # TODO: confirm that non-canonical names do not need to be sorted specially |
0 | 169 if name not in existing_sorted_names: |
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170 existing_sorted_names.append(name) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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171 |
0 | 172 if existing_sorted_names == current_order: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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173 shutil.move(unsorted_filename, fasta_filename) |
0 | 174 else: |
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175 _write_sorted_fasta(existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename) |
0 | 176 |
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177 |
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178 def _sort_fasta_custom(fasta_filename, params): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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179 (unsorted_filename, fasta_offsets, current_order) = _move_and_index_fasta_for_sorting(fasta_filename) |
0 | 180 sorted_names = [] |
181 for id_repeat in params['param_dict']['sorting']['sequence_identifiers']: | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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182 sorted_names.append(id_repeat['identifier']) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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183 handle_not_listed = params['param_dict']['sorting']['handle_not_listed_selector'] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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184 if handle_not_listed.startswith('keep'): |
0 | 185 add_list = [] |
186 for name in current_order: | |
187 if name not in sorted_names: | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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188 add_list.append(name) |
0 | 189 if add_list: |
190 if handle_not_listed == 'keep_append': | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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191 sorted_names.extend(add_list) |
0 | 192 else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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193 add_list.extend(sorted_names) |
0 | 194 sorted_names = add_list |
195 if sorted_names == current_order: | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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196 shutil.move(unsorted_filename, fasta_filename) |
0 | 197 else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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198 _write_sorted_fasta(sorted_names, fasta_offsets, fasta_filename, unsorted_filename) |
0 | 199 |
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200 |
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201 def _download_file(start, fh): |
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202 tmp = tempfile.NamedTemporaryFile() |
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203 tmp.write(start) |
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204 while True: |
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205 data = fh.read(CHUNK_SIZE) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8b8103fc4277014570a021cf3090b6986d17f7ff
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206 if data: |
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207 tmp.write(data) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8b8103fc4277014570a021cf3090b6986d17f7ff
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208 else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8b8103fc4277014570a021cf3090b6986d17f7ff
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209 break |
3
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210 tmp.flush() |
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211 tmp.seek(0) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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212 return tmp |
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213 |
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214 |
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215 def get_stream_reader(fh, tmp_dir): |
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216 """ |
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217 Check if file is compressed and return correct stream reader. |
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218 If file has to be downloaded, do it now. |
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219 """ |
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220 magic_dict = { |
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221 b"\x1f\x8b\x08": _get_stream_readers_for_gzip, |
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222 b"\x42\x5a\x68": _get_stream_readers_for_bz2, |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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223 b"\x50\x4b\x03\x04": _get_stream_readers_for_zip, |
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224 } |
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225 start_of_file = fh.read(CHUNK_SIZE) |
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226 try: |
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227 fh.seek(0) |
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228 except UnsupportedOperation: # This happens if fh has been created by urlopen |
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229 fh = _download_file(start_of_file, fh) |
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230 try: # Check if file is tar file |
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231 if tarfile.open(fileobj=StringIO(start_of_file)): |
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232 return _get_stream_readers_for_tar(fh, tmp_dir) |
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233 except tarfile.ReadError: |
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234 pass |
4
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235 for k, v in magic_dict.items(): |
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236 if start_of_file.startswith(k): |
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237 return v(fh, tmp_dir) |
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238 return [fh] |
3
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239 |
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240 |
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241 def _get_ucsc_download_address(params, dbkey): |
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242 """ |
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243 Check if we can find the correct file for the supplied dbkey on UCSC's FTP server |
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244 """ |
0 | 245 UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu' |
246 UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/' | |
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247 COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2'] |
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248 |
0 | 249 email = params['param_dict']['__user_email__'] |
250 if not email: | |
251 email = 'anonymous@example.com' | |
252 | |
253 ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey | |
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254 UCSC_CHROM_FA_FILENAMES = ['%s.chromFa' % ucsc_dbkey, 'chromFa', ucsc_dbkey] |
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255 |
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256 ftp = FTP(UCSC_FTP_SERVER) |
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257 ftp.login('anonymous', email) |
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258 |
0 | 259 ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey |
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260 path_contents = _get_files_in_ftp_path(ftp, ucsc_path) |
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261 ftp.quit() |
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262 |
0 | 263 for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES: |
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264 for ext in COMPRESSED_EXTENSIONS: |
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265 if "%s%s" % (ucsc_chrom_fa_filename, ext) in path_contents: |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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266 ucsc_file_name = "%s%s%s" % (ucsc_path, ucsc_chrom_fa_filename, ext) |
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267 return "ftp://%s%s" % (UCSC_FTP_SERVER, ucsc_file_name) |
0 | 268 |
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269 raise Exception('Unable to determine filename for UCSC Genome for %s: %s' % (ucsc_dbkey, path_contents)) |
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270 |
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271 |
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272 def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, **kwds): |
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273 fasta_filename = _stream_fasta_to_file(fasta_stream=fasta_readers, |
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274 target_directory=target_directory, |
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275 sequence_id=sequence_id) |
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276 sort_fasta(fasta_filename, params['param_dict']['sorting']['sort_selector'], params) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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277 if dbkey_name: |
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278 add_dbkey_to_table(data_manager_dict=data_manager_dict, |
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279 target_directory=target_directory, |
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280 dbkey=dbkey, |
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281 dbkey_name=dbkey_name, |
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282 fasta_filename=fasta_filename) |
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283 _add_data_table_entry(data_manager_dict, |
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284 data_table_entry=dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=os.path.basename(fasta_filename)), |
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285 data_table_name='all_fasta') |
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286 return fasta_filename |
0 | 287 |
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288 |
4
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289 def add_dbkey_to_table(data_manager_dict, target_directory, dbkey, dbkey_name, fasta_filename): |
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290 # do len calc here |
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291 len_base_name = "%s.len" % (dbkey) |
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292 compute_fasta_length(fasta_filename, os.path.join(target_directory, len_base_name), keep_first_word=True) |
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293 dbkey_dict = dict(value=dbkey, name=dbkey_name, len_path=len_base_name) |
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294 _add_data_table_entry(data_manager_dict, |
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295 data_table_entry=dbkey_dict, |
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296 data_table_name='__dbkeys__') |
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297 |
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298 |
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299 def download_from_ucsc(params, dbkey, tmp_dir, **kwds): |
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300 url = _get_ucsc_download_address(params, dbkey) |
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301 return get_stream_reader(urlopen(url), tmp_dir) |
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302 |
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303 |
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304 def download_from_ncbi(params, tmp_dir, **kwds): |
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305 NCBI_DOWNLOAD_URL = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' # FIXME: taken from dave's genome manager...why some japan site? |
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306 requested_identifier = params['param_dict']['reference_source']['requested_identifier'] |
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307 url = NCBI_DOWNLOAD_URL % requested_identifier |
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308 return get_stream_reader(urlopen(url), tmp_dir) |
0 | 309 |
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310 |
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311 def download_from_url(params, tmp_dir, **kwds): |
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312 """ |
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313 Download a file from a URL and return a list of filehandles from which to read the data. |
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314 |
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315 >>> tmp_dir = tempfile.mkdtemp() |
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316 >>> url = 'https://github.com/galaxyproject/tools-iuc/raw/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/test-data/test.tar.bz2' |
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317 >>> params = {'param_dict': {'reference_source': {'user_url': url}}} |
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318 >>> fh = download_from_url(params=params, tmp_dir=tmp_dir)[0][0] |
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319 >>> assert fh.readline().startswith('b>FBtr0304171') |
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320 >>> url = 'https://github.com/galaxyproject/tools-iuc/raw/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/test-data/phiX174.fasta' |
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321 >>> params = {'param_dict': {'reference_source': {'user_url': url}}} |
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322 >>> fh = download_from_url(params=params, tmp_dir=tmp_dir)[0][0] |
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323 >>> assert fh.readline().startswith('b>phiX174') |
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324 """ |
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325 urls = filter(bool, [x.strip() for x in params['param_dict']['reference_source']['user_url'].split('\n')]) |
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326 return [get_stream_reader(urlopen(url), tmp_dir) for url in urls] |
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327 |
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328 |
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329 def download_from_history(params, tmp_dir, **kwds): |
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330 # TODO: allow multiple FASTA input files |
0 | 331 input_filename = params['param_dict']['reference_source']['input_fasta'] |
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332 if isinstance(input_filename, list): |
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333 fasta_readers = [get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename] |
0 | 334 else: |
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335 fasta_readers = get_stream_reader(open(input_filename, 'rb'), tmp_dir) |
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336 return fasta_readers |
0 | 337 |
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338 |
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339 def copy_from_directory(data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir): |
0 | 340 input_filename = params['param_dict']['reference_source']['fasta_filename'] |
341 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink' | |
342 if create_symlink: | |
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343 data_table_entries = _create_symlink(input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name) |
0 | 344 else: |
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345 if isinstance(input_filename, list): |
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346 fasta_readers = [get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename] |
0 | 347 else: |
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348 fasta_readers = get_stream_reader(open(input_filename), tmp_dir) |
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349 return fasta_readers |
0 | 350 for data_table_name, data_table_entry in data_table_entries: |
351 if data_table_entry: | |
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352 _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name) |
0 | 353 |
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354 |
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355 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name): |
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356 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) |
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357 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get('all_fasta', []) |
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358 data_manager_dict['data_tables'][data_table_name].append(data_table_entry) |
0 | 359 return data_manager_dict |
360 | |
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361 |
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362 def _stream_fasta_to_file(fasta_stream, target_directory, sequence_id, close_stream=True): |
0 | 363 fasta_base_filename = "%s.fa" % sequence_id |
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364 fasta_filename = os.path.join(target_directory, fasta_base_filename) |
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365 with open(fasta_filename, 'wb+') as fasta_writer: |
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366 |
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367 if isinstance(fasta_stream, list) and len(fasta_stream) == 1: |
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368 fasta_stream = fasta_stream[0] |
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369 |
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370 if isinstance(fasta_stream, list): |
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371 last_char = None |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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372 for fh in fasta_stream: |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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373 if last_char not in [None, '\n', '\r', b'\n', b'\r']: |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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diff
changeset
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374 fasta_writer.write(b'\n') |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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375 while True: |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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376 data = fh.read(CHUNK_SIZE) |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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377 if data: |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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378 fasta_writer.write(data) |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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379 last_char = data[-1] |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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380 else: |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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381 break |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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382 if close_stream: |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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383 fh.close() |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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384 else: |
0 | 385 while True: |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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386 data = fasta_stream.read(CHUNK_SIZE) |
0 | 387 if data: |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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388 fasta_writer.write(data) |
0 | 389 else: |
390 break | |
391 if close_stream: | |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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392 fasta_stream.close() |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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393 return fasta_filename |
0 | 394 |
3
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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changeset
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395 |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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396 def compute_fasta_length(fasta_file, out_file, keep_first_word=False): |
0 | 397 infile = fasta_file |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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398 out = open(out_file, 'w') |
0 | 399 |
400 fasta_title = '' | |
401 seq_len = 0 | |
402 | |
403 first_entry = True | |
404 | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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405 for line in open(infile): |
0 | 406 line = line.strip() |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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407 if not line or line.startswith('#'): |
0 | 408 continue |
409 if line[0] == '>': | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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diff
changeset
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410 if not first_entry: |
0 | 411 if keep_first_word: |
412 fasta_title = fasta_title.split()[0] | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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413 out.write("%s\t%d\n" % (fasta_title[1:], seq_len)) |
0 | 414 else: |
415 first_entry = False | |
416 fasta_title = line | |
417 seq_len = 0 | |
418 else: | |
419 seq_len += len(line) | |
420 | |
421 # last fasta-entry | |
422 if keep_first_word: | |
423 fasta_title = fasta_title.split()[0] | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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424 out.write("%s\t%d\n" % (fasta_title[1:], seq_len)) |
0 | 425 out.close() |
426 | |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
devteam
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diff
changeset
|
427 |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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428 def _create_symlink(input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name): |
0 | 429 fasta_base_filename = "%s.fa" % sequence_id |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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430 fasta_filename = os.path.join(target_directory, fasta_base_filename) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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431 os.symlink(input_filename, fasta_filename) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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432 |
0 | 433 dbkey_dict = None |
434 if dbkey_name: | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
435 # do len calc here |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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436 len_base_name = "%s.len" % (dbkey) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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437 compute_fasta_length(fasta_filename, os.path.join(target_directory, len_base_name), keep_first_word=True) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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438 dbkey_dict = dict(value=dbkey, name=dbkey_name, len_path=len_base_name) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
|
439 |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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diff
changeset
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440 return [('__dbkeys__', dbkey_dict), ('all_fasta', dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename))] |
0 | 441 |
442 | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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changeset
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443 REFERENCE_SOURCE_TO_DOWNLOAD = dict(ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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444 directory=copy_from_directory) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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445 SORTING_METHODS = dict(as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom) |
0 | 446 |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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diff
changeset
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447 |
0 | 448 def main(): |
449 parser = optparse.OptionParser() | |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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450 parser.add_option('-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description') |
0 | 451 (options, args) = parser.parse_args() |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
452 |
0 | 453 filename = args[0] |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
454 |
8
14eb0fc65c62
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
iuc
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diff
changeset
|
455 with open(filename) as fh: |
14eb0fc65c62
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
iuc
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diff
changeset
|
456 params = json.load(fh) |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
|
457 target_directory = params['output_data'][0]['extra_files_path'] |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
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458 os.mkdir(target_directory) |
0 | 459 data_manager_dict = {} |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
460 |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
461 dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name(params, dbkey_description=options.dbkey_description) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
|
462 |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
|
463 if dbkey in [None, '', '?']: |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
464 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
devteam
parents:
1
diff
changeset
|
465 |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
devteam
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diff
changeset
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466 # Create a tmp_dir, in case a zip file needs to be uncompressed |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
devteam
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changeset
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467 tmp_dir = tempfile.mkdtemp() |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
468 # Fetch the FASTA |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
devteam
parents:
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diff
changeset
|
469 try: |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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470 reference_source = params['param_dict']['reference_source']['reference_source_selector'] |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
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471 fasta_readers = REFERENCE_SOURCE_TO_DOWNLOAD[reference_source](data_manager_dict=data_manager_dict, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
472 params=params, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
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473 target_directory=target_directory, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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474 dbkey=dbkey, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
|
475 dbkey_name=dbkey_name, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
|
476 sequence_id=sequence_id, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
changeset
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477 sequence_name=sequence_name, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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478 tmp_dir=tmp_dir) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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479 if fasta_readers: |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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480 add_fasta_to_table(data_manager_dict=data_manager_dict, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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481 fasta_readers=fasta_readers, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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482 target_directory=target_directory, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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483 dbkey=dbkey, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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484 dbkey_name=dbkey_name, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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485 sequence_id=sequence_id, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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486 sequence_name=sequence_name, |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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487 params=params) |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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488 |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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489 finally: |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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490 cleanup_before_exit(tmp_dir) |
4
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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491 # save info to json file |
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14eb0fc65c62
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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492 with open(filename, 'w') as fh: |
14eb0fc65c62
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"
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493 json.dump(data_manager_dict, fh, sort_keys=True) |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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494 |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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495 |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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496 if __name__ == "__main__": |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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497 main() |