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comparison data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py @ 0:f68a60c3d768 draft default tip

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author biocomp-ibens
date Wed, 16 May 2018 09:56:43 -0400
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-1:000000000000 0:f68a60c3d768
1 #!/usr/bin/python
2
3 import sys
4 import shutil
5 import re
6 import urllib2
7 import subprocess
8 import gzip
9 import os
10 import tempfile
11 from optparse import OptionParser
12 from galaxy.util.json import from_json_string, to_json_string
13
14 def get_arg():
15 parser = OptionParser()
16 parser.add_option("-e", "--ensembl", dest = 'ensembl_info', action = "store", nargs = 2, metavar = ("kingdom", "species_name"), type = "str")
17 parser.add_option("-o", "--output", dest='output_filename', action="store", nargs = 1, metavar = 'JSON_FILE')
18 parser.add_option("--log", dest='log_filename', action="store", nargs=1, metavar='log_report')
19 (options, args) = parser.parse_args()
20 return options, args
21
22 def cleanup_before_exit(tmp_dir):
23 if tmp_dir and os.path.exists(tmp_dir):
24 shutil.rmtree(tmp_dir)
25
26 def get_page_content(url):
27 req = urllib2.Request(url)
28 page = urllib2.urlopen(req)
29 return page.read()
30
31 def download_file(link, local_file_name):
32 req = urllib2.Request(link)
33 src_file = urllib2.urlopen(req)
34 local_file = open(local_file_name, 'wb')
35 local_file.write(src_file.read())
36 local_file.close()
37
38 def uncompress_gz(gz_file_name, uncompressed_file_name):
39 print("____________________________________________________________")
40 print("*** Uncompressing %s" % gz_file_name)
41 uncompressed_file = open(uncompressed_file_name, 'wb')
42 with gzip.open(gz_file_name, 'rb') as src_file:
43 uncompressed_file.write(src_file.read())
44 uncompressed_file.close()
45 print("-> Uncompressed !\n")
46
47 def add_data_table_entry( data_manager_dict, data_table_entry ):
48 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
49 data_manager_dict['data_tables']['alfa_indexes'] = data_manager_dict['data_tables'].get( 'alfa_indexes', data_table_entry )
50 return data_manager_dict
51
52 def standardize_species_name(species_name):
53 # substitute all capital letters, replace every succession of chars that are not letters to one underscore
54 standard_species_name = re.sub(r'[)]$', '', species_name)
55 standard_species_name = re.sub(r'[ _),-.(=]+ *', '_', standard_species_name)
56 return standard_species_name.lower()
57
58 def get_ensembl_url_root(kingdom):
59 print("____________________________________________________________")
60 print("*** Determining Ensembl ftp root url")
61 if kingdom == 'vertebrates':
62 root = 'ftp://ftp.ensembl.org/pub/current_gtf/'
63 else:
64 root = 'ftp://ftp.ensemblgenomes.org/pub/%s/current/' % kingdom
65 print("-> Determined !\n")
66 return root
67
68 def test_ensembl_species_exists(kingdom, url, species_name):
69 """
70 Test if a species exist on the ftp & return the species name with the species_line if so.
71 if the species_name matches a single string, then this string will be returned as the species name
72 if the species_name matches several strings, then an error is printed with all the possible species to enter for a new run
73 """
74 print("____________________________________________________________")
75 print ("*** Testing whether %s is referenced in Ensembl %s" % (species_name, kingdom))
76 list_species_file_name = 'species_Ensembl%s%s.txt' % (kingdom[0].upper(), kingdom[1:])
77 if kingdom=='vertebrates':
78 download_file(url, list_species_file_name)
79 else:
80 download_file(url + list_species_file_name, list_species_file_name)
81
82 grep_result = subprocess.Popen(['grep', species_name, list_species_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
83 species_lines_matched, grep_error = grep_result.communicate()
84 if grep_error != None or species_lines_matched == "":
85 msg = 'The species \'%s\' is not referenced on Ensembl (%s)' % (species_name, kingdom)
86 sys.exit(msg)
87
88 species_lines = species_lines_matched.split('\n')
89 del species_lines[-1]
90 nb_lines = len(species_lines)
91
92 if nb_lines == 1:
93 if kingdom == 'vertebrates':
94 fields = species_lines[0].split(' ')
95 columns = fields[-1].split('\r')
96 found_species_name = columns[0]
97 else:
98 columns = species_lines[0].split('\t')
99 found_species_name = columns[1]
100 if species_name != found_species_name:
101 print('-> \'%s\' has been replace with the complete species name \'%s\'' % (species_name, found_species_name))
102 return found_species_name, species_lines_matched
103 print("-> Referenced !\n")
104 return species_name, species_lines_matched
105 else:
106 list_species = [''] * nb_lines
107 for i in range(0, nb_lines):
108 if kingdom == 'vertebrates':
109 fields = species_lines[i].split(' ')
110 columns = fields[-1].split('\r')
111 list_species[i] = columns[0]
112 else:
113 columns = species_lines[i].split('\t')
114 list_species[i] = columns[1]
115 exact_match = re.search('^%s$' % species_name, list_species[i])
116 if exact_match:
117 print("-> Referenced !\n")
118 return species_name, species_lines[i]
119 msg = ("The string \'%s\' has been matched against the list of Ensembl Species but is not a complete species name.\n"
120 "Please retry with one of these following species names:\n" % species_name)
121 for s in list_species:
122 msg = ("%s- %s\n" % (msg, s))
123 sys.exit(msg)
124
125 def get_ensembl_collection(kingdom, species_line):
126 print("*** Extracting the %s_collection of the species" % kingdom)
127 collection_regex = re.compile('%s_.+_collection' % kingdom.lower())
128 collection_match = re.search(collection_regex, species_line)
129 if not collection_match:
130 print("-> Skiped: this species is not classified in a Ensembl %s collection\n" % kingdom)
131 return None
132 print("-> Extracted !\n")
133 return collection_match.group(0)
134
135 def get_ensembl_gtf_archive_name(url_dir, species_name):
136 print("____________________________________________________________")
137 print("*** Extracting the gtf archive name of %s" % species_name)
138 gtf_archive_regex = re.compile('%s\..*\.[0-9]+\.gtf\.gz' % species_name, flags = re.IGNORECASE)
139 dir_content = get_page_content(url_dir)
140 gtf_archive_match = re.search(gtf_archive_regex, dir_content)
141 if not gtf_archive_match:
142 sys.exit('The species is referenced on Ensembl but error of nomenclature led to download failure')
143 gtf_archive_name = gtf_archive_match.group(0)
144 print("-> Extracted !\n")
145 return gtf_archive_name
146
147 def get_ensembl_gtf_archive(kingdom, url, species_name, species_line):
148 if kingdom != 'vertebrates':
149 url = url + 'gtf/'
150 if kingdom == 'bacteria' or kingdom == 'protists' or kingdom == 'fungi':
151 collection = get_ensembl_collection(kingdom, species_line)
152 if collection != None:
153 url = url + "%s/" % collection
154 final_url = url + species_name + '/'
155 gtf_archive_name = get_ensembl_gtf_archive_name(final_url, species_name)
156 print("____________________________________________________________")
157 print("*** Download the gtf archive of %s" % species_name)
158 download_file(final_url + gtf_archive_name, gtf_archive_name)
159 print("-> Downloaded !\n")
160 return gtf_archive_name
161
162 def generate_alfa_indexes(path_to_alfa, gtf_file_name):
163 print("____________________________________________________________")
164 print("*** Generating alfa indexes from %s" % gtf_file_name)
165 alfa_result = subprocess.Popen(['python', path_to_alfa, '-a', gtf_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
166 alfa_out, alfa_err = alfa_result.communicate()
167 if alfa_err != None and not re.search('### End of program', alfa_err):
168 msg = 'Generation Failed due an alfa error: %s' % (alfa_err)
169 sys.exit(msg)
170 print("Alfa prompt:\n%s" % alfa_out)
171 print("-> Generated !\n")
172
173 def get_data_table_new_entry(gtf_archive_name):
174 info_list = gtf_archive_name.split('.')
175 species = info_list[0]
176 version = info_list[1]
177 release = info_list[2]
178 value = '%s_%s_%s' % (species, version, release)
179 dbkey = value
180 name = '%s: %s (release %s)' % (species, version, release)
181 prefix = '%s.%s.%s' % (species, version, release)
182 entry_dict = { 'species': species, 'version': version, 'release': release, 'value': value, 'dbkey': dbkey, 'name': name, 'prefix': prefix }
183 return entry_dict
184
185 def main():
186 options, args = get_arg()
187 tool_dir = args[0]
188
189 path_to_alfa = os.path.join(tool_dir, 'ALFA.py')
190
191 if options.output_filename == None:
192 msg = 'No json output file specified'
193 sys.exit(msg)
194 output_filename = options.output_filename
195
196 # Interestingly the output file to return is not empty initially.
197 # it contains a dictionary, with notably the path to the dir where the alfa_indexes
198 # are expected to be found
199 params = from_json_string(open(output_filename).read())
200 target_directory = params['output_data'][0]['extra_files_path']
201 os.mkdir(target_directory)
202
203 tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
204 os.chdir(tmp_dir)
205
206 data_manager_dict = {}
207
208 if options.ensembl_info:
209 kingdom, species_name = options.ensembl_info
210 species_name = standardize_species_name(species_name)
211 url = get_ensembl_url_root(kingdom)
212 species_name, species_line = test_ensembl_species_exists(kingdom, url, species_name)
213 gtf_archive_name = get_ensembl_gtf_archive(kingdom, url, species_name, species_line)
214 data_table_entry = get_data_table_new_entry(gtf_archive_name)
215 gtf_file_name = '%s.gtf' % data_table_entry['prefix']
216 uncompress_gz(gtf_archive_name, gtf_file_name)
217 generate_alfa_indexes(path_to_alfa, gtf_file_name)
218 stranded_index_name = '%s.stranded.index' % data_table_entry['prefix']
219 unstranded_index_name = '%s.unstranded.index' % data_table_entry['prefix']
220 add_data_table_entry(data_manager_dict, data_table_entry)
221
222 print("____________________________________________________________")
223 print("*** General Info")
224 print("URL ROOT:\t%s" % url)
225 print("SPECIES:\t%s" % data_table_entry['species'])
226 print("VERSION:\t%s" % data_table_entry['version'])
227 print("RELEASE:\t%s" % data_table_entry['release'])
228 print("VALUE:\t%s" % data_table_entry['value'])
229 print("DBKEY:\t%s" % data_table_entry['dbkey'])
230 print("NAME:\t%s" % data_table_entry['name'])
231 print("PREFIX:\t%s" % data_table_entry['prefix'])
232
233 shutil.move(stranded_index_name, os.path.join(target_directory, stranded_index_name))
234 shutil.move(unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
235
236 cleanup_before_exit(tmp_dir)
237
238 open(output_filename, 'wb').write(to_json_string(data_manager_dict))
239 main()