Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
annotate data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py @ 3:86fa71e9b427 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
author | devteam |
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date | Fri, 26 Aug 2016 12:46:47 -0400 |
parents | bca4c608408c |
children | 60994ca04177 |
rev | line source |
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0 | 1 #!/usr/bin/env python |
2 #Dan Blankenberg | |
3 | |
4 import sys | |
5 import os | |
6 import tempfile | |
7 import shutil | |
8 import optparse | |
9 from ftplib import FTP | |
10 import tarfile | |
11 import zipfile | |
12 import gzip | |
13 import bz2 | |
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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14 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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15 # 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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16 from urllib.request import urlopen |
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 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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18 from io import UnsupportedOperation |
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 except ImportError: |
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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20 # Fall back to Python 2's urllib2 |
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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21 from urllib2 import urlopen |
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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22 from StringIO import 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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23 UnsupportedOperation = AttributeError |
0 | 24 from json import loads, dumps |
25 | |
26 | |
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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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27 CHUNK_SIZE = 2**20 # 1mb |
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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28 |
0 | 29 |
30 def cleanup_before_exit( tmp_dir ): | |
31 if tmp_dir and os.path.exists( tmp_dir ): | |
32 shutil.rmtree( tmp_dir ) | |
33 | |
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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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34 |
0 | 35 def stop_err(msg): |
36 sys.stderr.write(msg) | |
37 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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38 |
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 |
0 | 40 def get_dbkey_dbname_id_name( params, dbkey_description=None ): |
41 dbkey = params['param_dict']['dbkey_source']['dbkey'] | |
42 #TODO: ensure sequence_id is unique and does not already appear in location file | |
43 sequence_id = params['param_dict']['sequence_id'] | |
44 if not sequence_id: | |
45 sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead? | |
46 | |
47 if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new': | |
48 dbkey_name = params['param_dict']['dbkey_source']['dbkey_name'] | |
49 if not dbkey_name: | |
50 dbkey_name = dbkey | |
51 else: | |
52 dbkey_name = None | |
53 | |
54 sequence_name = params['param_dict']['sequence_name'] | |
55 if not sequence_name: | |
56 sequence_name = dbkey_description | |
57 if not sequence_name: | |
58 sequence_name = dbkey | |
59 return dbkey, dbkey_name, sequence_id, sequence_name | |
60 | |
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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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61 |
0 | 62 def _get_files_in_ftp_path( ftp, path ): |
63 path_contents = [] | |
64 ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append ) | |
65 return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ] | |
66 | |
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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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67 |
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 def _get_stream_readers_for_tar( fh, tmp_dir ): |
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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69 fasta_tar = tarfile.open( fileobj=fh, mode='r:*' ) |
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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70 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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71 |
0 | 72 |
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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73 def _get_stream_readers_for_zip( fh, tmp_dir ): |
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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74 """ |
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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75 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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76 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
devteam
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changeset
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77 """ |
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 fasta_zip = zipfile.ZipFile( fh, 'r' ) |
0 | 79 rval = [] |
80 for member in fasta_zip.namelist(): | |
81 fasta_zip.extract( member, tmp_dir ) | |
82 rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) ) | |
83 return rval | |
84 | |
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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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85 |
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 def _get_stream_readers_for_gzip( fh, tmp_dir ): |
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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87 return [ gzip.GzipFile( fileobj=fh, mode='rb') ] |
0 | 88 |
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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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89 |
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 def _get_stream_readers_for_bz2( fh, tmp_dir ): |
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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91 return [ bz2.BZ2File( fh.name, 'rb') ] |
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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92 |
0 | 93 |
94 def sort_fasta( fasta_filename, sort_method, params ): | |
95 if sort_method is None: | |
96 return | |
97 assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method ) | |
98 return SORTING_METHODS[ sort_method ]( fasta_filename, params ) | |
99 | |
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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100 |
0 | 101 def _move_and_index_fasta_for_sorting( fasta_filename ): |
102 unsorted_filename = tempfile.NamedTemporaryFile().name | |
103 shutil.move( fasta_filename, unsorted_filename ) | |
104 fasta_offsets = {} | |
105 unsorted_fh = open( unsorted_filename ) | |
106 while True: | |
107 offset = unsorted_fh.tell() | |
108 line = unsorted_fh.readline() | |
109 if not line: | |
110 break | |
111 if line.startswith( ">" ): | |
112 line = line.split( None, 1 )[0][1:] | |
113 fasta_offsets[ line ] = offset | |
114 unsorted_fh.close() | |
115 current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) ) | |
116 return ( unsorted_filename, fasta_offsets, current_order ) | |
117 | |
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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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118 |
0 | 119 def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ): |
120 unsorted_fh = open( unsorted_fasta_filename ) | |
121 sorted_fh = open( sorted_fasta_filename, 'wb+' ) | |
122 | |
123 for name in sorted_names: | |
124 offset = fasta_offsets[ name ] | |
125 unsorted_fh.seek( offset ) | |
126 sorted_fh.write( unsorted_fh.readline() ) | |
127 while True: | |
128 line = unsorted_fh.readline() | |
129 if not line or line.startswith( ">" ): | |
130 break | |
131 sorted_fh.write( line ) | |
132 unsorted_fh.close() | |
133 sorted_fh.close() | |
134 | |
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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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135 |
0 | 136 def _sort_fasta_as_is( fasta_filename, params ): |
137 return | |
138 | |
139 def _sort_fasta_lexicographical( fasta_filename, params ): | |
140 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) | |
141 sorted_names = sorted( fasta_offsets.keys() ) | |
142 if sorted_names == current_order: | |
143 shutil.move( unsorted_filename, fasta_filename ) | |
144 else: | |
145 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) | |
146 | |
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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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147 |
0 | 148 def _sort_fasta_gatk( fasta_filename, params ): |
149 #This method was added by reviewer request. | |
150 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) | |
151 sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ] | |
152 #detect if we have chrN, or just N | |
153 has_chr = False | |
154 for chrom in sorted_names: | |
155 if "chr%s" % chrom in current_order: | |
156 has_chr = True | |
157 break | |
158 | |
159 if has_chr: | |
160 sorted_names = map( lambda x: "chr%s" % x, sorted_names) | |
161 sorted_names.insert( 0, "chrM" ) | |
162 else: | |
163 sorted_names.insert( 0, "MT" ) | |
164 sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) ) | |
165 | |
166 existing_sorted_names = [] | |
167 for name in sorted_names: | |
168 if name in current_order: | |
169 existing_sorted_names.append( name ) | |
170 for name in current_order: | |
171 #TODO: confirm that non-canonical names do not need to be sorted specially | |
172 if name not in existing_sorted_names: | |
173 existing_sorted_names.append( name ) | |
174 | |
175 if existing_sorted_names == current_order: | |
176 shutil.move( unsorted_filename, fasta_filename ) | |
177 else: | |
178 _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) | |
179 | |
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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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180 |
0 | 181 def _sort_fasta_custom( fasta_filename, params ): |
182 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) | |
183 sorted_names = [] | |
184 for id_repeat in params['param_dict']['sorting']['sequence_identifiers']: | |
185 sorted_names.append( id_repeat[ 'identifier' ] ) | |
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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186 handle_not_listed = params['param_dict']['sorting']['handle_not_listed_selector'] |
0 | 187 if handle_not_listed.startswith( 'keep' ): |
188 add_list = [] | |
189 for name in current_order: | |
190 if name not in sorted_names: | |
191 add_list.append( name ) | |
192 if add_list: | |
193 if handle_not_listed == 'keep_append': | |
194 sorted_names.extend( add_list ) | |
195 else: | |
196 add_list.extend( sorted_names ) | |
197 sorted_names = add_list | |
198 if sorted_names == current_order: | |
199 shutil.move( unsorted_filename, fasta_filename ) | |
200 else: | |
201 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) | |
202 | |
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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203 |
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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204 def _download_file(start, fh): |
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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205 tmp = tempfile.NamedTemporaryFile() |
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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206 tmp.write(start) |
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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207 tmp.write(fh.read()) |
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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208 tmp.flush() |
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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209 tmp.seek(0) |
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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210 return tmp |
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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211 |
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212 |
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213 def get_stream_reader(fh, tmp_dir): |
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214 """ |
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215 Check if file is compressed and return correct stream reader. |
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216 If file has to be downloaded, do it now. |
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217 """ |
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218 magic_dict = { |
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219 b"\x1f\x8b\x08": _get_stream_readers_for_gzip, |
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220 b"\x42\x5a\x68": _get_stream_readers_for_bz2, |
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221 b"\x50\x4b\x03\x04": _get_stream_readers_for_zip, |
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222 } |
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223 start_of_file = fh.read(CHUNK_SIZE) |
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224 try: |
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225 fh.seek(0) |
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226 except UnsupportedOperation: # This is if fh has been created by urlopen |
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227 fh = _download_file(start_of_file, fh) |
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228 for k,v in magic_dict.items(): |
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229 if start_of_file.startswith(k): |
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230 return v(fh, tmp_dir) |
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231 try: # Check if file is tar file |
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232 if tarfile.open(fileobj=StringIO(start_of_file)): |
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233 return _get_stream_readers_for_tar(fh, tmp_dir) |
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234 except tarfile.ReadError: |
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235 pass |
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236 return fh |
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237 |
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238 |
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239 def _get_ucsc_download_address(params, dbkey): |
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240 """ |
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241 Check if we can find the correct file for the supplied dbkey on UCSC's FTP server |
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242 """ |
0 | 243 UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu' |
244 UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/' | |
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245 COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2'] |
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246 |
0 | 247 email = params['param_dict']['__user_email__'] |
248 if not email: | |
249 email = 'anonymous@example.com' | |
250 | |
251 ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey | |
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252 UCSC_CHROM_FA_FILENAMES = ['%s.chromFa' % ucsc_dbkey, 'chromFa', ucsc_dbkey] |
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253 |
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254 ftp = FTP(UCSC_FTP_SERVER) |
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255 ftp.login('anonymous', email) |
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256 |
0 | 257 ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey |
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258 path_contents = _get_files_in_ftp_path(ftp, ucsc_path) |
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259 ftp.quit() |
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260 |
0 | 261 for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES: |
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262 for ext in COMPRESSED_EXTENSIONS: |
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263 if "%s%s" % (ucsc_chrom_fa_filename, ext) in path_contents: |
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264 ucsc_file_name = "%s%s%s" % (ucsc_path, ucsc_chrom_fa_filename, ext) |
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265 return "ftp://%s%s" % (UCSC_FTP_SERVER, ucsc_file_name) |
0 | 266 |
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267 raise Exception('Unable to determine filename for UCSC Genome for %s: %s' % (ucsc_dbkey, path_contents)) |
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268 |
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269 def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params): |
0 | 270 for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): |
271 if data_table_entry: | |
272 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) | |
273 | |
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274 |
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275 def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): |
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276 url = _get_ucsc_download_address(params, dbkey) |
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277 fasta_readers = get_stream_reader(urlopen(url), tmp_dir) |
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278 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params) |
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279 |
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280 |
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281 def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): |
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282 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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283 requested_identifier = params['param_dict']['reference_source']['requested_identifier'] |
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284 url = NCBI_DOWNLOAD_URL % requested_identifier |
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285 fasta_readers = get_stream_reader(urlopen(url), tmp_dir) |
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286 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params) |
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287 |
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288 |
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289 def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): |
0 | 290 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) ) |
3
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291 fasta_readers = [ get_stream_reader(urlopen( url ), tmp_dir) for url in urls ] |
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292 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params) |
0 | 293 |
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294 |
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295 def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): |
0 | 296 #TODO: allow multiple FASTA input files |
297 input_filename = params['param_dict']['reference_source']['input_fasta'] | |
298 if isinstance( input_filename, list ): | |
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299 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ] |
0 | 300 else: |
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301 fasta_readers = get_stream_reader(open(input_filename), tmp_dir) |
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302 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params) |
0 | 303 |
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304 |
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305 def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): |
0 | 306 input_filename = params['param_dict']['reference_source']['fasta_filename'] |
307 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink' | |
308 if create_symlink: | |
309 data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ) | |
310 else: | |
311 if isinstance( input_filename, list ): | |
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312 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ] |
0 | 313 else: |
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314 fasta_readers = get_stream_reader(open(input_filename), tmp_dir) |
0 | 315 data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ) |
316 for data_table_name, data_table_entry in data_table_entries: | |
317 if data_table_entry: | |
318 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) | |
319 | |
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320 |
0 | 321 def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ): |
322 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
323 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( 'all_fasta', [] ) | |
324 data_manager_dict['data_tables'][data_table_name].append( data_table_entry ) | |
325 return data_manager_dict | |
326 | |
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327 |
0 | 328 def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ): |
329 fasta_base_filename = "%s.fa" % sequence_id | |
330 fasta_filename = os.path.join( target_directory, fasta_base_filename ) | |
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331 with open( fasta_filename, 'wb+' ) as fasta_writer: |
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332 |
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333 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1: |
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334 fasta_stream = fasta_stream[0] |
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335 |
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336 if isinstance( fasta_stream, list ): |
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337 last_char = None |
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338 for fh in fasta_stream: |
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339 if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]: |
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340 fasta_writer.write( b'\n' ) |
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341 while True: |
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342 data = fh.read( CHUNK_SIZE ) |
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343 if data: |
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344 fasta_writer.write( data ) |
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345 last_char = data[-1] |
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346 else: |
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347 break |
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348 if close_stream: |
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349 fh.close() |
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350 else: |
0 | 351 while True: |
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352 data = fasta_stream.read( CHUNK_SIZE ) |
0 | 353 if data: |
354 fasta_writer.write( data ) | |
355 else: | |
356 break | |
357 if close_stream: | |
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358 fasta_stream.close() |
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359 |
0 | 360 sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params ) |
361 | |
362 dbkey_dict = None | |
363 if dbkey_name: | |
364 #do len calc here | |
365 len_base_name = "%s.len" % ( dbkey ) | |
366 compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True ) | |
367 dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name ) | |
368 | |
369 return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] | |
370 | |
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371 |
0 | 372 def compute_fasta_length( fasta_file, out_file, keep_first_word=False ): |
373 | |
374 infile = fasta_file | |
375 out = open( out_file, 'w') | |
376 | |
377 fasta_title = '' | |
378 seq_len = 0 | |
379 | |
380 first_entry = True | |
381 | |
382 for line in open( infile ): | |
383 line = line.strip() | |
384 if not line or line.startswith( '#' ): | |
385 continue | |
386 if line[0] == '>': | |
387 if first_entry == False: | |
388 if keep_first_word: | |
389 fasta_title = fasta_title.split()[0] | |
390 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) ) | |
391 else: | |
392 first_entry = False | |
393 fasta_title = line | |
394 seq_len = 0 | |
395 else: | |
396 seq_len += len(line) | |
397 | |
398 # last fasta-entry | |
399 if keep_first_word: | |
400 fasta_title = fasta_title.split()[0] | |
401 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) ) | |
402 out.close() | |
403 | |
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404 |
0 | 405 def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): |
406 fasta_base_filename = "%s.fa" % sequence_id | |
407 fasta_filename = os.path.join( target_directory, fasta_base_filename ) | |
408 os.symlink( input_filename, fasta_filename ) | |
409 | |
410 dbkey_dict = None | |
411 if dbkey_name: | |
412 #do len calc here | |
413 len_base_name = "%s.len" % ( dbkey ) | |
414 compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True ) | |
415 dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name ) | |
416 | |
417 return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] | |
418 | |
419 | |
420 REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory ) | |
421 | |
422 SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom ) | |
423 | |
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424 |
0 | 425 def main(): |
426 #Parse Command Line | |
427 parser = optparse.OptionParser() | |
428 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' ) | |
429 (options, args) = parser.parse_args() | |
430 | |
431 filename = args[0] | |
432 | |
433 params = loads( open( filename ).read() ) | |
434 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
435 os.mkdir( target_directory ) | |
436 data_manager_dict = {} | |
437 | |
438 dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description ) | |
439 | |
440 if dbkey in [ None, '', '?' ]: | |
441 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) | |
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442 |
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443 # Create a tmp_dir, in case a zip file needs to be uncompressed |
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444 tmp_dir = tempfile.mkdtemp() |
0 | 445 #Fetch the FASTA |
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446 try: |
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447 REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ) |
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448 finally: |
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449 cleanup_before_exit(tmp_dir) |
0 | 450 #save info to json file |
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451 open( filename, 'wb' ).write( dumps( data_manager_dict ).encode() ) |
0 | 452 |
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453 if __name__ == "__main__": |
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454 main() |