Mercurial > repos > jjohnson > gmap
annotate lib/galaxy/datatypes/gmap.py @ 10:93911bac43da
Modifications for ToolShed proprietary data types
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 05 Jan 2012 14:31:24 -0600 |
| parents | 3be0e0a858fe |
| children |
| rev | line source |
|---|---|
| 6 | 1 """ |
| 2 GMAP indexes | |
| 3 """ | |
| 4 import logging | |
| 5 import os,os.path,re | |
|
10
93911bac43da
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
6
diff
changeset
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6 import galaxy.datatypes.data |
|
93911bac43da
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
6
diff
changeset
|
7 from galaxy.datatypes.data import Text |
| 6 | 8 from galaxy import util |
|
10
93911bac43da
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
6
diff
changeset
|
9 from galaxy.datatypes.metadata import MetadataElement |
| 6 | 10 |
| 11 log = logging.getLogger(__name__) | |
| 12 | |
| 13 class GmapDB( Text ): | |
| 14 """ | |
| 15 A GMAP DB for indexes | |
| 16 """ | |
| 17 MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True ) | |
| 18 MetadataElement( name="basesize", default="12", desc="The basesize for offsetscomp", visible=True, readonly=True ) | |
| 19 MetadataElement( name="kmers", default=[''], desc="The kmer sizes for indexes", visible=True, no_value=[''], readonly=True ) | |
| 20 MetadataElement( name="map_dir", desc="The maps directory", default='unknown', set_in_upload=True, readonly=True ) | |
| 21 MetadataElement( name="maps", default=[''], desc="The names of maps stored for this gmap gmapdb", visible=True, no_value=[''], readonly=True ) | |
| 22 MetadataElement( name="snps", default=[''], desc="The names of SNP indexes stored for this gmapdb", visible=True, no_value=[''], readonly=True ) | |
| 23 MetadataElement( name="cmet", default=False, desc="Has a cmet index", visible=True, readonly=True ) | |
| 24 MetadataElement( name="atoi", default=False, desc="Has a atoi index", visible=True, readonly=True ) | |
| 25 | |
| 26 file_ext = 'gmapdb' | |
| 27 is_binary = True | |
| 28 composite_type = 'auto_primary_file' | |
| 29 allow_datatype_change = False | |
| 30 | |
| 31 def generate_primary_file( self, dataset = None ): | |
| 32 """ | |
| 33 This is called only at upload to write the html file | |
| 34 cannot rename the datasets here - they come with the default unfortunately | |
| 35 """ | |
| 36 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' | |
| 37 | |
| 38 def regenerate_primary_file(self,dataset): | |
| 39 """ | |
| 40 cannot do this until we are setting metadata | |
| 41 """ | |
| 42 bn = dataset.metadata.db_name | |
| 43 log.info( "GmapDB regenerate_primary_file %s" % (bn)) | |
| 44 rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)] | |
| 45 for i,name in enumerate(dataset.metadata.maps): | |
| 46 rval.append( '<li>%s' % name) | |
| 47 rval.append( '</ul></html>' ) | |
| 48 f = file(dataset.file_name,'w') | |
| 49 f.write("\n".join( rval )) | |
| 50 f.write('\n') | |
| 51 f.close() | |
| 52 | |
| 53 def set_peek( self, dataset, is_multi_byte=False ): | |
| 54 log.info( "GmapDB set_peek %s" % (dataset)) | |
| 55 if not dataset.dataset.purged: | |
| 56 dataset.peek = "GMAPDB index %s\n cmet %s\n atoi %s\n maps %s" % ( dataset.metadata.db_name,dataset.metadata.cmet,dataset.metadata.atoi,dataset.metadata.maps ) | |
| 57 dataset.blurb = "GMAPDB %s" % ( dataset.metadata.db_name ) | |
| 58 else: | |
| 59 dataset.peek = 'file does not exist' | |
| 60 dataset.blurb = 'file purged from disk' | |
| 61 def display_peek( self, dataset ): | |
| 62 try: | |
| 63 return dataset.peek | |
| 64 except: | |
| 65 return "GMAP index file" | |
| 66 | |
| 67 def sniff( self, filename ): | |
| 68 return False | |
| 69 def set_meta( self, dataset, overwrite = True, **kwd ): | |
| 70 """ | |
| 71 Expecting: | |
| 72 extra_files_path/<db_name>/db_name>.ref<basesize><kmer>3<index> | |
| 73 extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp | |
| 74 extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions | |
| 75 extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs | |
| 76 index maps: | |
| 77 extra_files_path/db_name/db_name.maps/*.iit | |
| 78 """ | |
| 79 log.info( "GmapDB set_meta %s %s" % (dataset,dataset.extra_files_path)) | |
| 80 pat = '(.*)\.((ref)|(met)[atgc][atgc]|(a2i)[atgc][atgc])((\d\d)(\d\d))?3positions(\.(.+))?' | |
| 81 efp = dataset.extra_files_path | |
| 82 flist = os.listdir(efp) | |
| 83 for i,fname in enumerate(flist): | |
| 84 log.info( "GmapDB set_meta %s %s" % (i,fname)) | |
| 85 fpath = os.path.join(efp,fname) | |
| 86 if os.path.isdir(fpath): | |
| 87 ilist = os.listdir(fpath) | |
| 88 kmers = {'':'default'} # HACK '' empty key added so user has default choice when selecting kmer from metadata | |
| 89 for j,iname in enumerate(ilist): | |
| 90 log.info( "GmapDB set_meta file %s %s" % (j,iname)) | |
| 91 ipath = os.path.join(fpath,iname) | |
| 92 if os.path.isdir(ipath): # find maps | |
| 93 dataset.metadata.map_dir = iname | |
| 94 for mapfile in os.listdir(ipath): | |
| 95 mapname = mapfile.replace('.iit','') | |
| 96 log.info( "GmapDB set_meta map %s %s" % (mapname,mapfile)) | |
| 97 dataset.metadata.maps.append(mapname) | |
| 98 else: | |
| 99 m = re.match(pat,iname) | |
| 100 if m: | |
| 101 log.info( "GmapDB set_meta m %s %s " % (iname, m)) | |
| 102 assert len(m.groups()) == 10 | |
| 103 dataset.metadata.db_name = fname | |
| 104 if m.groups()[2] == 'ref': | |
| 105 if m.groups()[-1] != None: | |
| 106 dataset.metadata.snps.append(m.groups()[-1]) | |
| 107 else: | |
| 108 if m.groups()[-3] != None: | |
| 109 k = int(m.groups()[-3]) | |
| 110 kmers[k] = k | |
| 111 if m.groups()[-4] != None: | |
| 112 dataset.metadata.basesize = int( m.groups()[-4]) | |
| 113 elif m.groups()[3] == 'met': | |
| 114 dataset.metadata.cmet = True | |
| 115 elif m.groups()[4] == 'a2i': | |
| 116 dataset.metadata.atoi = True | |
| 117 dataset.metadata.kmers = kmers.keys() | |
| 118 | |
| 119 class GmapSnpIndex( Text ): | |
| 120 """ | |
| 121 A GMAP SNP index created by snpindex | |
| 122 """ | |
| 123 MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True ) | |
| 124 MetadataElement( name="snps_name", default='snps', desc="The name of SNP index", visible=True, no_value='', readonly=True ) | |
| 125 | |
| 126 file_ext = 'gmapsnpindex' | |
| 127 is_binary = True | |
| 128 composite_type = 'auto_primary_file' | |
| 129 allow_datatype_change = False | |
| 130 | |
| 131 def generate_primary_file( self, dataset = None ): | |
| 132 """ | |
| 133 This is called only at upload to write the html file | |
| 134 cannot rename the datasets here - they come with the default unfortunately | |
| 135 """ | |
| 136 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' | |
| 137 | |
| 138 def regenerate_primary_file(self,dataset): | |
| 139 """ | |
| 140 cannot do this until we are setting metadata | |
| 141 """ | |
| 142 bn = dataset.metadata.db_name | |
| 143 log.info( "GmapDB regenerate_primary_file %s" % (bn)) | |
| 144 rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)] | |
| 145 for i,name in enumerate(dataset.metadata.maps): | |
| 146 rval.append( '<li>%s' % name) | |
| 147 rval.append( '</ul></html>' ) | |
| 148 f = file(dataset.file_name,'w') | |
| 149 f.write("\n".join( rval )) | |
| 150 f.write('\n') | |
| 151 f.close() | |
| 152 def set_peek( self, dataset, is_multi_byte=False ): | |
| 153 log.info( "GmapSnpIndex set_peek %s" % (dataset)) | |
| 154 if not dataset.dataset.purged: | |
| 155 dataset.peek = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name) | |
| 156 dataset.blurb = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name) | |
| 157 else: | |
| 158 dataset.peek = 'file does not exist' | |
| 159 dataset.blurb = 'file purged from disk' | |
| 160 def display_peek( self, dataset ): | |
| 161 try: | |
| 162 return dataset.peek | |
| 163 except: | |
| 164 return "GMAP SNP index" | |
| 165 | |
| 166 def sniff( self, filename ): | |
| 167 return False | |
| 168 def set_meta( self, dataset, overwrite = True, **kwd ): | |
| 169 """ | |
| 170 Expecting: | |
| 171 extra_files_path/snp_name.iit | |
| 172 extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp.snp_name | |
| 173 extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions.snp_name | |
| 174 extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs.snp_name | |
| 175 """ | |
| 176 log.info( "GmapSnpIndex set_meta %s %s" % (dataset,dataset.extra_files_path)) | |
| 177 pat = '(.*)\.(ref((\d\d)(\d\d))?3positions)\.(.+)?' | |
| 178 efp = dataset.extra_files_path | |
| 179 flist = os.listdir(efp) | |
| 180 for i,fname in enumerate(flist): | |
| 181 m = re.match(pat,fname) | |
| 182 if m: | |
| 183 assert len(m.groups()) == 6 | |
| 184 dataset.metadata.db_name = m.groups()[0] | |
| 185 dataset.metadata.snps_name = m.groups()[-1] | |
| 186 | |
| 187 | |
| 188 | |
| 189 | |
| 190 class IntervalIndexTree( Text ): | |
| 191 """ | |
| 192 A GMAP Interval Index Tree Map | |
| 193 created by iit_store | |
| 194 (/path/to/map)/(mapname).iit | |
| 195 """ | |
| 196 file_ext = 'iit' | |
| 197 is_binary = True | |
| 198 | |
| 199 class SpliceSitesIntervalIndexTree( IntervalIndexTree ): | |
| 200 """ | |
| 201 A GMAP Interval Index Tree Map | |
| 202 created by iit_store | |
| 203 """ | |
| 204 file_ext = 'splicesites.iit' | |
| 205 | |
| 206 class IntronsIntervalIndexTree( IntervalIndexTree ): | |
| 207 """ | |
| 208 A GMAP Interval Index Tree Map | |
| 209 created by iit_store | |
| 210 """ | |
| 211 file_ext = 'introns.iit' | |
| 212 | |
| 213 class SNPsIntervalIndexTree( IntervalIndexTree ): | |
| 214 """ | |
| 215 A GMAP Interval Index Tree Map | |
| 216 created by iit_store | |
| 217 """ | |
| 218 file_ext = 'snps.iit' | |
| 219 | |
| 220 class TallyIntervalIndexTree( IntervalIndexTree ): | |
| 221 """ | |
| 222 A GMAP Interval Index Tree Map | |
| 223 created by iit_store | |
| 224 """ | |
| 225 file_ext = 'tally.iit' | |
| 226 | |
| 227 class IntervalAnnotation( Text ): | |
| 228 """ | |
| 229 Class describing a GMAP Interval format: | |
| 230 >label coords optional_tag | |
| 231 optional_annotation (which may be zero, one, or multiple lines) | |
| 232 The coords should be of the form: | |
| 233 chr:position | |
| 234 chr:startposition..endposition | |
| 235 """ | |
| 236 file_ext = 'gmap_annotation' | |
| 237 """Add metadata elements""" | |
| 238 MetadataElement( name="annotations", default=0, desc="Number of interval annotations", readonly=True, optional=True, visible=False, no_value=0 ) | |
| 239 | |
| 240 def set_meta( self, dataset, **kwd ): | |
| 241 """ | |
| 242 Set the number of annotations and the number of data lines in dataset. | |
| 243 """ | |
| 244 data_lines = 0 | |
| 245 annotations = 0 | |
| 246 for line in file( dataset.file_name ): | |
| 247 line = line.strip() | |
| 248 if line and line.startswith( '>' ): | |
| 249 annotations += 1 | |
| 250 data_lines +=1 | |
| 251 else: | |
| 252 data_lines += 1 | |
| 253 dataset.metadata.data_lines = data_lines | |
| 254 dataset.metadata.annotations = annotations | |
| 255 def set_peek( self, dataset, is_multi_byte=False ): | |
| 256 if not dataset.dataset.purged: | |
| 257 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) | |
| 258 if dataset.metadata.annotations: | |
| 259 dataset.blurb = "%s annotations" % util.commaify( str( dataset.metadata.annotations ) ) | |
| 260 else: | |
| 261 dataset.blurb = data.nice_size( dataset.get_size() ) | |
| 262 else: | |
| 263 dataset.peek = 'file does not exist' | |
| 264 dataset.blurb = 'file purged from disk' | |
| 265 | |
| 266 def sniff( self, filename ): | |
| 267 """ | |
| 268 Determines whether the file is a gmap annotation file | |
| 269 Format: | |
| 270 >label coords optional_tag | |
| 271 optional_annotation (which may be zero, one, or multiple lines) | |
| 272 For example, the label may be an EST accession, with the coords | |
| 273 representing its genomic position. Labels may be duplicated if | |
| 274 necessary. | |
| 275 The coords should be of the form | |
| 276 chr:position | |
| 277 chr:startposition..endposition | |
| 278 The term "chr:position" is equivalent to "chr:position..position". If | |
| 279 you want to indicate that the interval is on the minus strand or | |
| 280 reverse direction, then <endposition> may be less than <startposition>. | |
| 281 """ | |
| 282 try: | |
| 283 pat = '>(\S+)\s((\S+):(\d+)(\.\.(\d+))?(\s.(.+))?$' #>label chr:position[..endposition][ optional_tag] | |
| 284 fh = open( filename ) | |
| 285 count = 0 | |
| 286 while True and count < 10: | |
| 287 line = fh.readline() | |
| 288 if not line: | |
| 289 break #EOF | |
| 290 line = line.strip() | |
| 291 if line: #first non-empty line | |
| 292 if line.startswith( '>' ): | |
| 293 count += 1 | |
| 294 if re.match(pat,line) == None: # Failed to match | |
| 295 return False | |
| 296 finally: | |
| 297 fh.close() | |
| 298 return False | |
| 299 | |
| 300 class SpliceSiteAnnotation(IntervalAnnotation): | |
| 301 file_ext = 'gmap_splicesites' | |
| 302 """ | |
| 303 Example: | |
| 304 >NM_004448.ERBB2.exon1 17:35110090..35110091 donor 6678 | |
| 305 >NM_004448.ERBB2.exon2 17:35116768..35116769 acceptor 6678 | |
| 306 >NM_004448.ERBB2.exon2 17:35116920..35116921 donor 1179 | |
| 307 >NM_004448.ERBB2.exon3 17:35118099..35118100 acceptor 1179 | |
| 308 >NM_004449.ERG.exon1 21:38955452..38955451 donor 783 | |
| 309 >NM_004449.ERG.exon2 21:38878740..38878739 acceptor 783 | |
| 310 >NM_004449.ERG.exon2 21:38878638..38878637 donor 360 | |
| 311 >NM_004449.ERG.exon3 21:38869542..38869541 acceptor 360 | |
| 312 Each line must start with a ">" character, then be followed by an | |
| 313 identifier, which may have duplicates and can have any format, with | |
| 314 the gene name or exon number shown here only as a suggestion. Then | |
| 315 there should be the chromosomal coordinates which straddle the | |
| 316 exon-intron boundary, so one coordinate is on the exon and one is on | |
| 317 the intron. (Coordinates are all 1-based, so the first character of a | |
| 318 chromosome is number 1.) Finally, there should be the splice type: | |
| 319 "donor" or "acceptor". You may optionally store the intron distance | |
| 320 at the end. GSNAP can use this intron distance, if it is longer than | |
| 321 its value for --localsplicedist, to look for long introns at that | |
| 322 splice site. The same splice site may have different intron distances | |
| 323 in the database; GSNAP will use the longest intron distance reported | |
| 324 in searching for long introns. | |
| 325 """ | |
| 326 def sniff( self, filename ): # TODO | |
| 327 """ | |
| 328 Determines whether the file is a gmap splice site annotation file | |
| 329 """ | |
| 330 try: | |
| 331 pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+))\s(donor|acceptor)(\s(\d+))?$' #>label chr:position..position donor|acceptor[ intron_dist] | |
| 332 fh = open( filename ) | |
| 333 count = 0 | |
| 334 while True and count < 10: | |
| 335 line = fh.readline() | |
| 336 if not line: | |
| 337 break #EOF | |
| 338 line = line.strip() | |
| 339 if line: #first non-empty line | |
| 340 count += 1 | |
| 341 if re.match(pat,line) == None: # Failed to match | |
| 342 return False | |
| 343 finally: | |
| 344 fh.close() | |
| 345 return False | |
| 346 | |
| 347 class IntronAnnotation(IntervalAnnotation): | |
| 348 file_ext = 'gmap_introns' | |
| 349 """ | |
| 350 Example: | |
| 351 >NM_004448.ERBB2.intron1 17:35110090..35116769 | |
| 352 >NM_004448.ERBB2.intron2 17:35116920..35118100 | |
| 353 >NM_004449.ERG.intron1 21:38955452..38878739 | |
| 354 >NM_004449.ERG.intron2 21:38878638..38869541 | |
| 355 The coordinates are 1-based, and specify the exon coordinates | |
| 356 surrounding the intron, with the first coordinate being from the donor | |
| 357 exon and the second one being from the acceptor exon. | |
| 358 """ | |
| 359 def sniff( self, filename ): # TODO | |
| 360 """ | |
| 361 Determines whether the file is a gmap Intron annotation file | |
| 362 """ | |
| 363 try: | |
| 364 pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+)(\s(.)+)?$' #>label chr:position | |
| 365 fh = open( filename ) | |
| 366 count = 0 | |
| 367 while True and count < 10: | |
| 368 line = fh.readline() | |
| 369 if not line: | |
| 370 break #EOF | |
| 371 line = line.strip() | |
| 372 if line: #first non-empty line | |
| 373 count += 1 | |
| 374 if re.match(pat,line) == None: # Failed to match | |
| 375 return False | |
| 376 finally: | |
| 377 fh.close() | |
| 378 return False | |
| 379 | |
| 380 class SNPAnnotation(IntervalAnnotation): | |
| 381 file_ext = 'gmap_snps' | |
| 382 """ | |
| 383 Example: | |
| 384 >rs62211261 21:14379270 CG | |
| 385 >rs62211262 21:14379281 AT | |
| 386 >rs62211263 21:14379298 WN | |
| 387 Each line must start with a ">" character, then be followed by an | |
| 388 identifier (which may have duplicates). Then there should be the | |
| 389 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so | |
| 390 the first character of a chromosome is number 1.) Finally, there | |
| 391 should be the two possible alleles. (Previous versions required that | |
| 392 these be in alphabetical order: "AC", "AG", "AT", "CG", "CT", or "GT", | |
| 393 but that is no longer a requirement.) These alleles must correspond | |
| 394 to the possible nucleotides on the plus strand of the genome. If the | |
| 395 one of these two letters does not match the allele in the reference | |
| 396 sequence, that SNP will be ignored in subsequent processing as a | |
| 397 probable error. | |
| 398 | |
| 399 GSNAP also supports the idea of a wildcard SNP. A wildcard SNP allows | |
| 400 all nucleotides to match at that position, not just a given reference | |
| 401 and alternate allele. It is essentially as if an "N" were recorded at | |
| 402 that genomic location, although the index files still keep track of | |
| 403 the reference allele. To indicate that a position has a wildcard SNP, | |
| 404 you can indicate the genotype as "WN", where "W" is the reference | |
| 405 allele. Another indication of a wildcard SNP is to provide two | |
| 406 separate lines at that position with the genotypes "WX" and "WY", | |
| 407 where "W" is the reference allele and "X" and "Y" are two different | |
| 408 alternate alleles. | |
| 409 """ | |
| 410 def sniff( self, filename ): | |
| 411 """ | |
| 412 Determines whether the file is a gmap SNP annotation file | |
| 413 """ | |
| 414 try: | |
| 415 pat = '>(\S+)\s((\S+):(\d+)\s([TACGW][TACGN])$' #>label chr:position ATCG | |
| 416 fh = open( filename ) | |
| 417 count = 0 | |
| 418 while True and count < 10: | |
| 419 line = fh.readline() | |
| 420 if not line: | |
| 421 break #EOF | |
| 422 line = line.strip() | |
| 423 if line: #first non-empty line | |
| 424 count += 1 | |
| 425 if re.match(pat,line) == None: # Failed to match | |
| 426 return False | |
| 427 finally: | |
| 428 fh.close() | |
| 429 return False | |
| 430 | |
| 431 | |
| 432 class TallyAnnotation(IntervalAnnotation): | |
| 433 file_ext = 'gsnap_tally' | |
| 434 """ | |
| 435 Output produced by gsnap_tally | |
| 436 Example: | |
| 437 >144 chr20:57268791..57268935 | |
| 438 G0 | |
| 439 A1(1@7|1Q-3) | |
| 440 A2(1@36,1@1|1Q2,1Q-8) | |
| 441 C2 0.889,0.912,0.889,0.889,0.933,0.912,0.912,0.889,0.889,0.889 -2.66,-2.89,-2.66,-2.66,-3.16,-2.89,-2.89,-2.66,-2.66,-2.66 | |
| 442 C1 T1 0.888,0.9,0.888,0.9,0.913,0.9,0.911,0.888,0.9,0.913 -2.66,-2.78,-2.66,-2.78,-2.91,-2.78,-2.89,-2.66,-2.78,-2.91 | |
| 443 """ | |
| 444 def sniff( self, filename ): # TODO | |
| 445 """ | |
| 446 Determines whether the file is a gmap splice site annotation file | |
| 447 """ | |
| 448 try: | |
| 449 pat = '^>(\d+)\s((\S+):(\d+)\.\.(\d+))$' #>total chr:position..position | |
| 450 pat2 = '^[GATCN]\d.*$' #BaseCountDeatails | |
| 451 fh = open( filename ) | |
| 452 count = 0 | |
| 453 while True and count < 10: | |
| 454 line = fh.readline() | |
| 455 if not line: | |
| 456 break #EOF | |
| 457 line = line.strip() | |
| 458 if line: #first non-empty line | |
| 459 count += 1 | |
| 460 if re.match(pat,line) == None and re.match(pat2,line) == None: # Failed to match | |
| 461 return False | |
| 462 finally: | |
| 463 fh.close() | |
| 464 return False | |
| 465 | |
| 466 class GsnapResult( Text ): | |
| 467 """ | |
| 468 The default output format for gsnap. Can be used as input for gsnap_tally. | |
| 469 """ | |
| 470 file_ext = 'gsnap' | |
| 471 | |
| 472 |