Package Bio :: Package UniGene
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Source Code for Package Bio.UniGene

  1  # Copyright 2006 by Sean Davis.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5  # 
  6  # $Id: __init__.py,v 1.12 2009-04-24 12:03:45 mdehoon Exp $ 
  7  # Sean Davis <sdavis2 at mail dot nih dot gov> 
  8  # National Cancer Institute 
  9  # National Institutes of Health 
 10  # Bethesda, MD, USA 
 11  # 
 12   
 13  """Parse Unigene flat file format files such as the Hs.data file. 
 14   
 15  Here is an overview of the flat file format that this parser deals with: 
 16     Line types/qualifiers: 
 17   
 18         ID           UniGene cluster ID 
 19         TITLE        Title for the cluster 
 20         GENE         Gene symbol 
 21         CYTOBAND     Cytological band 
 22         EXPRESS      Tissues of origin for ESTs in cluster 
 23         RESTR_EXPR   Single tissue or development stage contributes 
 24                      more than half the total EST frequency for this gene. 
 25         GNM_TERMINUS genomic confirmation of presence of a 3' terminus; 
 26                      T if a non-templated polyA tail is found among 
 27                      a cluster's sequences; else 
 28                      I if templated As are found in genomic sequence or 
 29                      S if a canonical polyA signal is found on 
 30                        the genomic sequence 
 31         GENE_ID      Entrez gene identifier associated with at least one 
 32                      sequence in this cluster; 
 33                      to be used instead of LocusLink. 
 34         LOCUSLINK    LocusLink identifier associated with at least one 
 35                      sequence in this cluster; 
 36                      deprecated in favor of GENE_ID 
 37         HOMOL        Homology; 
 38         CHROMOSOME   Chromosome.  For plants, CHROMOSOME refers to mapping 
 39                      on the arabidopsis genome. 
 40         STS          STS 
 41              ACC=         GenBank/EMBL/DDBJ accession number of STS 
 42                           [optional field] 
 43              UNISTS=      identifier in NCBI's UNISTS database 
 44         TXMAP        Transcript map interval 
 45              MARKER=      Marker found on at least one sequence in this 
 46                           cluster 
 47              RHPANEL=     Radiation Hybrid panel used to place marker 
 48         PROTSIM      Protein Similarity data for the sequence with 
 49                      highest-scoring protein similarity in this cluster 
 50              ORG=         Organism 
 51              PROTGI=      Sequence GI of protein 
 52              PROTID=      Sequence ID of protein 
 53              PCT=         Percent alignment 
 54              ALN=         length of aligned region (aa) 
 55         SCOUNT       Number of sequences in the cluster 
 56         SEQUENCE     Sequence 
 57              ACC=         GenBank/EMBL/DDBJ accession number of sequence 
 58              NID=         Unique nucleotide sequence identifier (gi) 
 59              PID=         Unique protein sequence identifier (used for 
 60                           non-ESTs) 
 61              CLONE=       Clone identifier (used for ESTs only) 
 62              END=         End (5'/3') of clone insert read (used for 
 63                           ESTs only) 
 64              LID=         Library ID; see Hs.lib.info for library name 
 65                           and tissue 
 66              MGC=         5' CDS-completeness indicator; if present, the 
 67                           clone associated with this sequence is believed 
 68                           CDS-complete. A value greater than 511 is the gi 
 69                           of the CDS-complete mRNA matched by the EST, 
 70                           otherwise the value is an indicator of the 
 71                           reliability of the test indicating CDS 
 72                           completeness; higher values indicate more 
 73                           reliable CDS-completeness predictions. 
 74             SEQTYPE=      Description of the nucleotide sequence. 
 75                           Possible values are mRNA, EST and HTC. 
 76             TRACE=        The Trace ID of the EST sequence, as provided by 
 77                           NCBI Trace Archive 
 78  """ 
 79   
 80   
81 -class SequenceLine(object):
82 """Store the information for one SEQUENCE line from a Unigene file 83 84 Initialize with the text part of the SEQUENCE line, or nothing. 85 86 Attributes and descriptions (access as LOWER CASE) 87 ACC= GenBank/EMBL/DDBJ accession number of sequence 88 NID= Unique nucleotide sequence identifier (gi) 89 PID= Unique protein sequence identifier (used for non-ESTs) 90 CLONE= Clone identifier (used for ESTs only) 91 END= End (5'/3') of clone insert read (used for ESTs only) 92 LID= Library ID; see Hs.lib.info for library name and tissue 93 MGC= 5' CDS-completeness indicator; if present, 94 the clone associated with this sequence 95 is believed CDS-complete. A value greater than 511 96 is the gi of the CDS-complete mRNA matched by the EST, 97 otherwise the value is an indicator of the reliability 98 of the test indicating CDS completeness; 99 higher values indicate more reliable CDS-completeness 100 predictions. 101 SEQTYPE= Description of the nucleotide sequence. Possible values 102 are mRNA, EST and HTC. 103 TRACE= The Trace ID of the EST sequence, as provided by NCBI 104 Trace Archive 105 """ 106
107 - def __init__(self,text=None):
108 self.acc = '' 109 self.nid = '' 110 self.lid = '' 111 self.pid = '' 112 self.clone = '' 113 self.image = '' 114 self.is_image = False 115 self.end = '' 116 self.mgc = '' 117 self.seqtype = '' 118 self.trace = '' 119 if text is not None: 120 self.text=text 121 self._init_from_text(text)
122
123 - def _init_from_text(self, text):
124 parts = text.split('; ') 125 for part in parts: 126 key, val = part.split("=") 127 if key=='CLONE': 128 if val[:5]=='IMAGE': 129 self.is_image=True 130 self.image = val[6:] 131 setattr(self, key.lower(), val)
132
133 - def __repr__(self):
134 return self.text
135 136
137 -class ProtsimLine(object):
138 """Store the information for one PROTSIM line from a Unigene file 139 140 Initialize with the text part of the PROTSIM line, or nothing. 141 142 Attributes and descriptions (access as LOWER CASE) 143 ORG= Organism 144 PROTGI= Sequence GI of protein 145 PROTID= Sequence ID of protein 146 PCT= Percent alignment 147 ALN= length of aligned region (aa) 148 """ 149
150 - def __init__(self,text=None):
151 self.org = '' 152 self.protgi = '' 153 self.protid = '' 154 self.pct = '' 155 self.aln = '' 156 if text is not None: 157 self.text=text 158 self._init_from_text(text)
159
160 - def _init_from_text(self, text):
161 parts = text.split('; ') 162 163 for part in parts: 164 key, val = part.split("=") 165 setattr(self, key.lower(), val)
166
167 - def __repr__(self):
168 return self.text
169 170
171 -class STSLine(object):
172 """Store the information for one STS line from a Unigene file 173 174 Initialize with the text part of the STS line, or nothing. 175 176 Attributes and descriptions (access as LOWER CASE) 177 178 ACC= GenBank/EMBL/DDBJ accession number of STS [optional field] 179 UNISTS= identifier in NCBI's UNISTS database 180 """ 181
182 - def __init__(self,text=None):
183 self.acc = '' 184 self.unists = '' 185 if text is not None: 186 self.text=text 187 self._init_from_text(text)
188
189 - def _init_from_text(self, text):
190 parts = text.split(' ') 191 192 for part in parts: 193 key, val = part.split("=") 194 setattr(self, key.lower(), val)
195
196 - def __repr__(self):
197 return self.text
198 199
200 -class Record(object):
201 """Store a Unigene record 202 203 Here is what is stored: 204 205 self.ID = '' # ID line 206 self.species = '' # Hs, Bt, etc. 207 self.title = '' # TITLE line 208 self.symbol = '' # GENE line 209 self.cytoband = '' # CYTOBAND line 210 self.express = [] # EXPRESS line, parsed on ';' 211 # Will be an array of strings 212 self.restr_expr = '' # RESTR_EXPR line 213 self.gnm_terminus = '' # GNM_TERMINUS line 214 self.gene_id = '' # GENE_ID line 215 self.locuslink = '' # LOCUSLINK line 216 self.homol = '' # HOMOL line 217 self.chromosome = '' # CHROMOSOME line 218 self.protsim = [] # PROTSIM entries, array of Protsims 219 # Type ProtsimLine 220 self.sequence = [] # SEQUENCE entries, array of Sequence entries 221 # Type SequenceLine 222 self.sts = [] # STS entries, array of STS entries 223 # Type STSLine 224 self.txmap = [] # TXMAP entries, array of TXMap entries 225 """ 226
227 - def __init__(self):
228 self.ID = '' # ID line 229 self.species = '' # Hs, Bt, etc. 230 self.title = '' # TITLE line 231 self.symbol = '' # GENE line 232 self.cytoband = '' # CYTOBAND line 233 self.express = [] # EXPRESS line, parsed on ';' 234 self.restr_expr = '' # RESTR_EXPR line 235 self.gnm_terminus = '' # GNM_TERMINUS line 236 self.gene_id = '' # GENE_ID line 237 self.locuslink = '' # LOCUSLINK line 238 self.homol = '' # HOMOL line 239 self.chromosome = '' # CHROMOSOME line 240 self.protsim = [] # PROTSIM entries, array of Protsims 241 self.sequence = [] # SEQUENCE entries, array of Sequence entries 242 self.sts = [] # STS entries, array of STS entries 243 self.txmap = [] # TXMAP entries, array of TXMap entries
244
245 - def __repr__(self):
246 return "<%s> %s %s\n%s" % (self.__class__.__name__, 247 self.ID, self.symbol, self.title)
248 249
250 -def parse(handle):
251 while True: 252 record = _read(handle) 253 if not record: 254 return 255 yield record
256 257
258 -def read(handle):
259 record = _read(handle) 260 if not record: 261 raise ValueError("No SwissProt record found") 262 # We should have reached the end of the record by now 263 remainder = handle.read() 264 if remainder: 265 raise ValueError("More than one SwissProt record found") 266 return record
267 268 269 # Everything below is private 270 271
272 -def _read(handle):
273 UG_INDENT = 12 274 record = None 275 for line in handle: 276 tag, value = line[:UG_INDENT].rstrip(), line[UG_INDENT:].rstrip() 277 line = line.rstrip() 278 if tag=="ID": 279 record = Record() 280 record.ID = value 281 record.species = record.ID.split('.')[0] 282 elif tag=="TITLE": 283 record.title = value 284 elif tag=="GENE": 285 record.symbol = value 286 elif tag=="GENE_ID": 287 record.gene_id = value 288 elif tag=="LOCUSLINK": 289 record.locuslink = value 290 elif tag=="HOMOL": 291 if value=="YES": 292 record.homol = True 293 elif value=="NO": 294 record.homol = True 295 else: 296 raise ValueError("Cannot parse HOMOL line %s" % line) 297 elif tag=="EXPRESS": 298 record.express = [word.strip() for word in value.split("|")] 299 elif tag=="RESTR_EXPR": 300 record.restr_expr = [word.strip() for word in value.split("|")] 301 elif tag=="CHROMOSOME": 302 record.chromosome = value 303 elif tag=="CYTOBAND": 304 record.cytoband = value 305 elif tag=="PROTSIM": 306 protsim = ProtsimLine(value) 307 record.protsim.append(protsim) 308 elif tag=="SCOUNT": 309 scount = int(value) 310 elif tag=="SEQUENCE": 311 sequence = SequenceLine(value) 312 record.sequence.append(sequence) 313 elif tag=="STS": 314 sts = STSLine(value) 315 record.sts.append(sts) 316 elif tag=='//': 317 if len(record.sequence)!=scount: 318 raise ValueError("The number of sequences specified in the record" 319 " (%d) does not agree with the number of sequences found (%d)" % (scount, len(record.sequence))) 320 return record 321 else: 322 raise ValueError("Unknown tag %s" % tag) 323 if record: 324 raise ValueError("Unexpected end of stream.")
325