Source Code for Module biana.BianaParser.ipiParser

  1  """ 
  2      BIANA: Biologic Interactions and Network Analysis 
  3      Copyright (C) 2009  Javier Garcia-Garcia, Emre Guney, Baldo Oliva 
  4   
  5      This program is free software: you can redistribute it and/or modify 
  6      it under the terms of the GNU General Public License as published by 
  7      the Free Software Foundation, either version 3 of the License, or 
  8      (at your option) any later version. 
  9   
 10      This program is distributed in the hope that it will be useful, 
 11      but WITHOUT ANY WARRANTY; without even the implied warranty of 
 12      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
 13      GNU General Public License for more details. 
 14   
 15      You should have received a copy of the GNU General Public License 
 16      along with this program.  If not, see <http://www.gnu.org/licenses/>. 
 17   
 18  """ 
 19   
 20   
 21  """ 
 22  File        : ipi2piana.py 
 23  Author      : Javier Garcia 
 24  Creation    : November 2007 
 25  Contents    : fills up tables in database piana with information from IPI 
 26  Called from :  
 27  ======================================================================================================= 
 28  """ 
 29   
 30  import re 
 31  from bianaParser import * 
 32   
 33   
 34 -class IPIParser(BianaParser): 
 35      """ 
 36      IPI Parser Class 
 37      """ 
 38   
 39      name = "ipi" 
 40      description = "Inserts information of IPI database into BIANA" 
 41      external_entity_definition = "External entities are proteins" 
 42      external_entity_relations = "" 
 43   
 44 -    def __init__(self): 
 45   
 46          # Start with the default values 
 47   
 48          BianaParser.__init__(self, default_db_description = "IPI. International Protein Index", 
 49                               default_script_name = "ipi2piana.py", 
 50                               default_script_description = IPIParser.description, 
 51                               additional_compulsory_arguments = []) 
 52          self.default_eE_attribute = "ipi" 
 53   
 54   
 55 -    def parse_database(self): 
 56   
 57          self.initialize_input_file_descriptor() 
 58   
 59          if self.input_file_fd is not None: 
 60              self.parse_file() 
 61          else:  # is a directory 
 62              dirname = os.path.dirname(self.input_file+os.sep)+os.sep 
 63              files = os.listdir(self.input_file) 
 64              for current_file in files: 
 65                  if re.search("ipi.\w+\.fasta",current_file): 
 66                      if ( current_file.endswith(".gz") ): 
 67                          self.input_file_fd = gzip.open(dirname+current_file,'r') 
 68                      else: 
 69                          self.input_file_fd = file(dirname+current_file, 'r') 
 70                      self.parse_file() 
 71   
 72   
 73 -    def parse_file(self): 
 74          """ 
 75          Method that implements the specific operations of HGNC parser 
 76          """ 
 77   
 78          # Example: 
 79   
 80          #>IPI:IPI00000001.2|SWISS-PROT:O95793-1|TREMBL:Q59F99|ENSEMBL:ENSP00000360922;ENSP00000379466|REFSEQ:NP_059347|H-INV:HIT000329496|VEGA:OTTHUMP00000031233 Tax 
 81          #_Id=9606 Gene_Symbol=STAU1 Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1 
 82          #MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS 
 83          #ITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF 
 84   
 85   
 86          line_number = 0 
 87          ipi_object = None 
 88          ipi_object_number = 0 
 89          actual_sequence = [] 
 90   
 91          for line in self.input_file_fd: 
 92   
 93              line_number += 1 
 94   
 95              line.strip() 
 96   
 97              field_search_re = re.compile("([\w\-]+)\:(\S+)") 
 98              tax_id_regex = re.compile("Tax_Id=(\d+)") 
 99              gene_symbol_regex = re.compile("Gene_Symbol=(\S+)\s+(.*)") 
100   
101              if line[0]=='>': 
102   
103   
104                  # Insert the last entry to the database 
105                  if ipi_object is not None: 
106                      ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="proteinSequence",  
107                                                                       value = ProteinSequence("".join(actual_sequence)))) 
108   
109                      self.biana_access.insert_new_external_entity( externalEntity = ipi_object ) 
110   
111                  # Start new entry 
112                  ipi_object = ExternalEntity( source_database = self.database, type="protein" ) 
113                  ipi_object_number += 1 
114   
115                  if self.time_control: 
116                      if ipi_object_number%20000==0: 
117                          sys.stderr.write("%s entries done in %s seconds\n" %(ipi_object_number,time.time()-self.initial_time)) 
118   
119                  actual_sequence = [] 
120                  line_fields = line.lstrip(">").split("|") 
121   
122                  for actual_field in line_fields: 
123                       
124                      search = field_search_re.search(actual_field) 
125                       
126                      if search: 
127                          identifier_type = search.group(1) 
128                          values = search.group(2).split(";") 
129   
130                          if( identifier_type == "IPI" ): 
131                              for actual_value in values: 
132                                  #if actual_value.startswith("IPI"): 
133                                  #    actual_value = actual_value[3:] 
134                                  ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier = "ipi",  
135                                                                                   value = actual_value, 
136                                                                                   type = "unique" )) 
137                       
138                          elif( identifier_type == "ENSEMBL" ): 
139                              for actual_value in values: 
140                                  ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="ensembl",  
141                                                                                   value = actual_value, 
142                                                                                   type = "cross-reference" )) 
143   
144                          elif( identifier_type == "REFSEQ" ): 
145                              for actual_value in values: 
146                                  ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="refseq",  
147                                                                                   value = actual_value, 
148                                                                                   type = "cross-reference" )) 
149   
150                          elif( identifier_type == "TREMBL" ): 
151                              for actual_value in values: 
152                                  ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="uniprotaccession",  
153                                                                                   value = actual_value, 
154                                                                                   type = "cross-reference" )) 
155   
156                          elif( identifier_type == "SWISS-PROT" ): 
157                              for actual_value in values: 
158                                  ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="UniprotAccession",  
159                                                                                   value = actual_value[0:6], 
160                                                                                   type = "cross-reference" )) 
161   
162                          elif( identifier_type == "TAIR" ): 
163                              for actual_value in values: 
164                                  ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="tair",  
165                                                                                   value = actual_value, 
166                                                                                   type = "cross-reference" )) 
167   
168                  search = tax_id_regex.search(line) 
169                  if search: 
170                      ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="taxID", 
171                                                                       value = search.group(1) )) 
172   
173                  search = gene_symbol_regex.search(line) 
174                  if search: 
175                      ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="geneSymbol", 
176                                                                       value = actual_value, 
177                                                                       type = "cross-reference" )) 
178   
179                      search2 = re.search("[Emb|Gb]\|(\S+)",search.group(2)) 
180                      if search2: 
181                          ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier = "accessionNumber", 
182                                                                           value = search2.group(1), 
183                                                                           type = "cross-reference" )) 
184                      else: 
185                          ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="description", 
186                                                                           value = search.group(2) )) 
187   
188              else: 
189                  # Sequence line 
190                  actual_sequence.append(line.strip()) 
191   
192          # Insert the last entry 
193          if ipi_object is not None: 
194              ipi_object.add_attribute(ExternalEntityAttribute(attribute_identifier="proteinSequence",  
195                                                               value = ProteinSequence("".join(actual_sequence)))) 
196              self.biana_access.insert_new_external_entity( externalEntity = ipi_object ) 
197