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1 #!/usr/bin/python
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2
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3 import sys
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4 import shutil
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5 import re
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6 import urllib2
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7 import subprocess
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8 import gzip
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9 import os
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10 import tempfile
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11 from optparse import OptionParser
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12 from galaxy.util.json import from_json_string, to_json_string
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13
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14 def get_arg():
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15 parser = OptionParser()
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16 parser.add_option("-e", "--ensembl", dest = 'ensembl_info', action = "store", nargs = 2, metavar = ("kingdom", "species_name"), type = "str")
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17 parser.add_option("-o", "--output", dest='output_filename', action="store", nargs = 1, metavar = 'JSON_FILE')
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18 parser.add_option("--log", dest='log_filename', action="store", nargs=1, metavar='log_report')
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19 (options, args) = parser.parse_args()
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20 return options, args
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21
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22 def cleanup_before_exit(tmp_dir):
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23 if tmp_dir and os.path.exists(tmp_dir):
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24 shutil.rmtree(tmp_dir)
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25
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26 def get_page_content(url):
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27 req = urllib2.Request(url)
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28 page = urllib2.urlopen(req)
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29 return page.read()
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30
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31 def download_file(link, local_file_name):
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32 req = urllib2.Request(link)
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33 src_file = urllib2.urlopen(req)
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34 local_file = open(local_file_name, 'wb')
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35 local_file.write(src_file.read())
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36 local_file.close()
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37
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38 def uncompress_gz(gz_file_name, uncompressed_file_name):
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39 print("____________________________________________________________")
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40 print("*** Uncompressing %s" % gz_file_name)
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41 uncompressed_file = open(uncompressed_file_name, 'wb')
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42 with gzip.open(gz_file_name, 'rb') as src_file:
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43 uncompressed_file.write(src_file.read())
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44 uncompressed_file.close()
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45 print("-> Uncompressed !\n")
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46
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47 def standardize_species_name(species_name):
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48 #substitute all capital letters, replace every succession of chars that are not letters to one underscore
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49 standard_species_name = re.sub(r'[)]$', '', species_name)
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50 standard_species_name = re.sub(r'[ _),-.(=]+ *', '_', standard_species_name)
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51 return standard_species_name.lower()
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52
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53 def get_ensembl_url_root(kingdom):
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54 print("____________________________________________________________")
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55 print("*** Determining Ensembl ftp root url")
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56 if kingdom == 'vertebrates':
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57 root = 'ftp://ftp.ensembl.org/pub/current_gtf/'
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58 else:
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59 root = 'ftp://ftp.ensemblgenomes.org/pub/%s/current/' % kingdom
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60 print("-> Determined !\n")
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61 return root
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62
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63 def test_ensembl_species_exists(kingdom, url, species_name):
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64 """
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65 Test if a species exist on the ftp & return the species name with the species_line if so.
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66 if the species_name matches a single string, then this string will be returned as the species name
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67 if the species_name matches several strings, then an error is printed with all the possible species to enter for a new run
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68 """
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69 print("____________________________________________________________")
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70 print ("*** Testing whether %s is referenced in Ensembl %s" % (species_name, kingdom))
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71 list_species_file_name = 'species_Ensembl%s%s.txt' % (kingdom[0].upper(), kingdom[1:])
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72 if kingdom=='vertebrates':
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73 download_file(url, list_species_file_name)
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74 else:
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75 download_file(url + list_species_file_name, list_species_file_name)
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76
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77 grep_result = subprocess.Popen(['grep', species_name, list_species_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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78 species_lines_matched, grep_error = grep_result.communicate()
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79 if grep_error != None or species_lines_matched == "":
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80 msg = 'The species \'%s\' is not referenced on Ensembl (%s)' % (species_name, kingdom)
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81 sys.exit(msg)
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82
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83 species_lines = species_lines_matched.split('\n')
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84 del species_lines[-1]
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85 nb_lines = len(species_lines)
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86
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87 if nb_lines == 1:
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88 if kingdom == 'vertebrates':
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89 fields = species_lines[0].split(' ')
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90 columns = fields[-1].split('\r')
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91 found_species_name = columns[0]
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92 else:
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93 columns = species_lines[0].split('\t')
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94 found_species_name = columns[1]
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95 if species_name != found_species_name:
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96 print('-> \'%s\' has been replace with the complete species name \'%s\'' % (species_name, found_species_name))
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97 return found_species_name, species_lines_matched
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98 print("-> Referenced !\n")
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99 return species_name, species_lines_matched
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100 else:
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101 list_species = [''] * nb_lines
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102 for i in range(0, nb_lines):
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103 if kingdom == 'vertebrates':
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104 fields = species_lines[i].split(' ')
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105 columns = fields[-1].split('\r')
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106 list_species[i] = columns[0]
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107 else:
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108 columns = species_lines[i].split('\t')
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109 list_species[i] = columns[1]
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110 exact_match = re.search('^%s$' % species_name, list_species[i])
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111 if exact_match:
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112 print("-> Referenced !\n")
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113 return species_name, species_lines[i]
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114 msg = ("The string \'%s\' has been matched against the list of Ensembl Species but is not a complete species name.\n"
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115 "Please retry with one of these following species names:\n" % species_name)
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116 for s in list_species:
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117 msg = ("%s- %s\n" % (msg, s))
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118 sys.exit(msg)
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119
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120 def get_ensembl_collection(kingdom, species_line):
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121 print("*** Extracting the %s_collection of the species" % kingdom)
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122 collection_regex = re.compile('%s_.+_collection' % kingdom.lower())
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123 collection_match = re.search(collection_regex, species_line)
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124 if not collection_match:
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125 print("-> Skiped: this species is not classified in a Ensembl %s collection\n" % kingdom)
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126 return None
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127 print("-> Extracted !\n")
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128 return collection_match.group(0)
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129
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130 def get_ensembl_gtf_archive_name(url_dir, species_name):
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131 print("____________________________________________________________")
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132 print("*** Extracting the gtf archive name of %s" % species_name)
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133 gtf_archive_regex = re.compile('%s\..*\.[0-9]+\.gtf\.gz' % species_name, flags = re.IGNORECASE)
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134 chr_gtf_archive_regex = re.compile('%s\..*\.[0-9]+\.chr\.gtf\.gz' % species_name, flags = re.IGNORECASE)
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135 dir_content = get_page_content(url_dir)
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136 gtf_archive_match = re.search(gtf_archive_regex, dir_content)
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137 chr_gtf_archive_match = re.search(chr_gtf_archive_regex, dir_content)
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138 if not gtf_archive_match:
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139 sys.exit('The species is referenced on Ensembl but error of nomenclature led to download failure')
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140 if not chr_gtf_archive_match:
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141 chr_gtf_archive_name = ""
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142 else:
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143 chr_gtf_archive_name = chr_gtf_archive_match.group(0)
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144 gtf_archive_name = gtf_archive_match.group(0)
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145 print("-> Extracted !\n")
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146 return gtf_archive_name, chr_gtf_archive_name
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147
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148 def get_ensembl_gtf_archive(kingdom, url, species_name, species_line):
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149 if kingdom != 'vertebrates':
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150 url = url + 'gtf/'
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151 if kingdom == 'bacteria' or kingdom == 'protists' or kingdom == 'fungi':
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152 collection = get_ensembl_collection(kingdom, species_line)
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153 if collection != None:
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154 url = url + "%s/" % collection
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155 final_url = url + species_name + '/'
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156 gtf_archive_name, chr_gtf_archive_name = get_ensembl_gtf_archive_name(final_url, species_name)
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157 print("____________________________________________________________")
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158 print("*** Download the gtf archive of %s" % species_name)
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159 download_file(final_url + gtf_archive_name, gtf_archive_name)
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160 print("-> Downloaded !\n")
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161 if chr_gtf_archive_name:
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162 print("*** Download the chr gtf archive of %s" % species_name)
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163 download_file(final_url + chr_gtf_archive_name, chr_gtf_archive_name)
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164 print("-> Downloaded !\n")
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165 return gtf_archive_name, chr_gtf_archive_name
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166
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167 def generate_alfa_indexes(path_to_alfa, gtf_file_name):
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168 print("____________________________________________________________")
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169 print("*** Generating alfa indexes from %s" % gtf_file_name)
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170 alfa_result = subprocess.Popen(['python', path_to_alfa, '-a', gtf_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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171 alfa_out, alfa_err = alfa_result.communicate()
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172 if alfa_err != None and not re.search('### End of program', alfa_err):
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173 msg = 'Generation Failed due an alfa error: %s' % (alfa_err)
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174 sys.exit(msg)
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175 print("Alfa prompt:\n%s" % alfa_out)
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176 print("-> Generated !\n")
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177
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178 def get_data_table_new_entry(gtf_archive_name):
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179 info_list = gtf_archive_name.split('.')
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180 species = info_list[0]
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181 version = info_list[1]
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182 release = info_list[2]
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183 value = '%s_%s_%s' % (species, version, release)
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184 dbkey = value
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185 name = '%s: %s (release %s)' % (species, version, release)
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186 prefix = '%s.%s.%s' % (species, version, release)
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187 entry_dict = { 'species': species, 'version': version, 'release': release, 'value': value, 'dbkey': dbkey, 'name': name, 'prefix': prefix }
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188 return entry_dict
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189
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190 def chr_get_data_table_new_entry(chr_gtf_archive_name):
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191 info_list = chr_gtf_archive_name.split('.')
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192 species = info_list[0]
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193 version = info_list[1]
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194 release = info_list[2]
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195 value = '%s_%s_%s.chr' % (species, version, release)
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196 dbkey = value
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197 name = '%s: %s (release %s) - Chr' % (species, version, release)
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198 prefix = '%s.%s.%s.chr' % (species, version, release)
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199 entry_dict = { 'species': species, 'version': version, 'release': release, 'value': value, 'dbkey': dbkey, 'name': name, 'prefix': prefix }
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200 return entry_dict
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201
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202 def main():
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203 options, args = get_arg()
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204 tool_dir = args[0]
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205
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206 path_to_alfa = os.path.join(tool_dir, 'ALFA.py')
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207
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208 if options.output_filename == None:
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209 msg = 'No json output file specified'
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210 sys.exit(msg)
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211 output_filename = options.output_filename
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212
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213 # Interestingly the output file to return is not empty initially.
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214 # it contains a dictionary, with notably the path to the dir where the alfa_indexes
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215 # are expected to be found
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216 params = from_json_string(open(output_filename).read())
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217 target_directory = params['output_data'][0]['extra_files_path']
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218 os.mkdir(target_directory)
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219
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220 tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
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221 os.chdir(tmp_dir)
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222
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223 data_manager_dict = {}
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224 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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225 data_manager_dict['data_tables']['alfa_indexes'] = data_manager_dict['data_tables'].get('alfa_indexes', [])
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226
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227 if options.ensembl_info:
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228 kingdom, species_name = options.ensembl_info
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229 species_name = standardize_species_name(species_name)
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230 url = get_ensembl_url_root(kingdom)
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231 species_name, species_line = test_ensembl_species_exists(kingdom, url, species_name)
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232 gtf_archive_name, chr_gtf_archive_name = get_ensembl_gtf_archive(kingdom, url, species_name, species_line)
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233 data_table_entry = get_data_table_new_entry(gtf_archive_name)
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234 gtf_file_name = '%s.gtf' % data_table_entry['prefix']
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235 uncompress_gz(gtf_archive_name, gtf_file_name)
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236 generate_alfa_indexes(path_to_alfa, gtf_file_name)
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237 stranded_index_name = '%s.stranded.index' % data_table_entry['prefix']
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238 unstranded_index_name = '%s.unstranded.index' % data_table_entry['prefix']
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239 data_manager_dict['data_tables']['alfa_indexes'].append(data_table_entry)
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240 if chr_gtf_archive_name:
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241 data_table_entry = chr_get_data_table_new_entry(chr_gtf_archive_name)
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242 chr_gtf_file_name = '%s.gtf' % data_table_entry['prefix']
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243 uncompress_gz(chr_gtf_archive_name, chr_gtf_file_name)
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244 generate_alfa_indexes(path_to_alfa, chr_gtf_file_name)
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245 chr_stranded_index_name = '%s.stranded.index' % data_table_entry['prefix']
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246 chr_unstranded_index_name = '%s.unstranded.index' % data_table_entry['prefix']
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247 data_manager_dict['data_tables']['alfa_indexes'].append(data_table_entry)
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248
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249
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250 print("____________________________________________________________")
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251 print("*** General Info")
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252 print("URL ROOT:\t%s" % url)
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253 print("SPECIES:\t%s" % data_table_entry['species'])
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254 print("VERSION:\t%s" % data_table_entry['version'])
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255 print("RELEASE:\t%s" % data_table_entry['release'])
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256 print("VALUE:\t%s" % data_table_entry['value'])
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257 print("DBKEY:\t%s" % data_table_entry['dbkey'])
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258 print("NAME:\t%s" % data_table_entry['name'])
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259 print("PREFIX:\t%s" % data_table_entry['prefix'])
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260
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261 shutil.copyfile(stranded_index_name, os.path.join(target_directory, stranded_index_name))
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262 shutil.copyfile(unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
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263
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264 if chr_gtf_archive_name:
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265 shutil.copyfile(chr_stranded_index_name, os.path.join(target_directory, stranded_index_name))
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266 shutil.copyfile(chr_unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
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267
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268
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269 cleanup_before_exit(tmp_dir)
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270
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271 open(output_filename, 'wb').write(to_json_string(data_manager_dict))
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272 main()
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