def close(self,commitData=True):
"""Close method which performs updating the docstrings and creating the schema objects."""
print "# Finalizing mapping schema(s)..."
if self._closed == True:
return
# UPDATE DOC STRING FOR forward MAPPING
self.Mf.__doc__ = "Mapping resource (forward) between annotations %s and %s" % (self.Mf.sourceDB._persistent_id,
self.Mf.targetDB._persistent_id)
#UPDATE OUR METABASE WITH THE RESOURCE STRING FOR THE MAPPING
worldbase.add_resource(self.resourceString+"_forward", self.Mf)
# FOR forward MAPPING
forward_bindAttrs = (self.forwardAttr, self.inverseAttr) # self.inverseAttr is either None or set to an appropriate inverse attribute
relationF = metabase.OneToManyRelation(self.Mf.sourceDB, self.Mf.targetDB, bindAttrs=forward_bindAttrs)
relationF.__doc__ = "Mapping schema (forward) between annotations %s and %s" % (self.Mf.sourceDB._persistent_id,
self.Mf.targetDB._persistent_id)
# UPDATE OUR SCHEMA WITH THE RESOURCE STRING FOR THE MAPPING
worldbase.add_schema(self.resourceString+"_forward", relationF)
# HANDLE REVERSE MAPPING AND SCHEMA
relationR = None
if self.Mr != None:
# UPDATE DOC STRING FOR reverse MAPPING
self.Mr.__doc__ = "Mapping resource (reverse) between annotations %s and %s" % (self.Mr.sourceDB._persistent_id,
self.Mr.targetDB._persistent_id)
#UPDATE OUR METABASE WITH THE RESOURCE STRING FOR THE MAPPING
worldbase.add_resource(self.resourceString+"_reverse", self.Mr)
# FOR reverse MAPPING
reverse_bindAttrs = (self.reverseAttr, None)
relationR = metabase.OneToManyRelation(self.Mr.sourceDB, self.Mr.targetDB, bindAttrs=reverse_bindAttrs)
relationR.__doc__ = "Mapping schema (reverse) between annotations %s and %s" % (self.Mr.sourceDB._persistent_id, # Use self.Mf for consistent
self.Mr.targetDB._persistent_id) # doc strings with forward mapping
# UPDATE OUR SCHEMA WITH THE RESOURCE STRING FOR THE MAPPING
worldbase.add_schema(self.resourceString+"_reverse", relationR)
if(commitData==True):
print "# Committing to worldbase: (1) %s (2) %s" % (str(self.Mf.__doc__),str(self.Mr.__doc__))
worldbase.commit()
print "# Closing mapping object(s)"
# FLUSH MAPPING(S) TO PERSISTENT STORAGE
self.Mf.close()
if self.Mr:
self.Mr.close()
# Set closed flag
self._closed = True
def main():
"""Build an annotation from the given gff file
"""
usage = """Build and save the annotations defined in the given gff files
Saves an annotationDB (representing the file itself) and creates a mapping
in the form genome[chromosome][100:200].officialGenes"""
parser = optparse.OptionParser("%prog [options] data1.gff [data2.gff ...]\n"+usage)
parser.add_option("--genome_resource", '-g', dest="genome_resource", type="string",
help="""The pygr resource for the genome, eg, 'Bio.Seq.Genome.TRICA.triCas3'""")
#parser.add_option("--annotationDB_resource", '-a', dest="annotationDB_resource", type="string",
#help="""Where to save the created annotationDB. eg,
#Bio.Annotation.TRICA.triCas3.officialGenes""")
parser.add_option("--sqlDB_resource", '-s', dest="sqlDB_resource", type="string",
help="""Where to save the created sqlDB and a unique file name eg,
Bio.Annotation.TRICA.triCas3.features_sqlDB,gffDB_v1""")
parser.add_option("--save_pathstem", '-p', dest="pathstem", type="string",
help="""The file to save the resource to, eg,
'/home/baldig/projects/genomics/pygrdata/annotations/fly/triCas3_official_genes'""")
parser.add_option("--map_resource", '-m', dest="map_resource", type="string",
help="""the resource to save the annotationDB->Genome map,
saved both to worldbase and to worldbase.schema, eg,
'Bio.Annotation.TRICA.triCas3.BeetleBase.officialGenesMap""")
parser.add_option("--bind_attribute", '-b', dest="bind_attribute", type="string",
help="""The attribute to access annotationDB from genome region, eg,
'officialGenes' would be accessible via triCas3['ChLG2'][100:200].officialGenes
Default is not to bind an attribute to genome""")
(opts, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
print 'Please specify at least one gff file to read'
sys.exit(-1)
if None in [opts.genome_resource, opts.pathstem, opts.map_resource]:
parser.print_help()
print 'Required options: genome_resource, sqlDB_resource, pathstem, map_resource'
sys.exit(-1)
if opts.sqlDB_resource.count(',') != 1:
parser.print_help()
print 'Error: sqlDB_resource must be comma separated string with exactly one comma.'
else:
opts.sqlDB_resource = opts.sqlDB_resource.split(',')
try :
w = worldbase(opts.sqlDB_resource[0])
parser.print_help()
print "Warning: sqlDB_resource already exists. Please select a new name."
exit(-1)
except WorldbaseNotFoundError:
pass
print '# Loading original genome db'
genome = worldbase(opts.genome_resource)
#annotDB = annotation.AnnotationDB(None, genome, opts.bind_attribute,
#filename=opts.pathstem + '_annotDB', mode='c', verbose=False)
sqlDB = sqlgraph.SQLiteServerInfo('%s/%s.sqlite' %(opts.pathstem,opts.sqlDB_resource[1]))
gff2lite = simpleGFF2PygrSQLite(sqlDB)
nlmsa = cnestedlist.NLMSA(opts.pathstem, 'w', pairwiseMode=True, bidirectional=False)
for filename in args:
print '# adding to sqlDB from %s' % filename
gff2lite.update(filename)
tableNames = gff2lite.getTableNames()
for table in tableNames:
#for row in read_for_pygr(fileIn):
#curAnnot = annotDB.new_annotation(index, row)
#nlmsa.addAnnotation(curAnnot)
#index += 1
#annotDB.close() # Flush annotation data to disk
print '# building NLMSA from all gff files'
nlmsa.build(saveSeqDict=True)
print '# saving annotationDB and NLMSA to worldbase as %s and %s' % (opts.annotationDB_resource,
opts.map_resource)
annotDB.__doc__ = 'Combined gff annotationDB from files %s on genome %s' % (', '.join(args),
opts.genome_resource)
nlmsa.__doc__ = 'Mapping of %s, from gff files %s onto genome %s' % (opts.annotationDB_resource,
', '.join(args),
opts.genome_resource)
worldbase.add_resource(opts.annotationDB_resource, annotDB)
worldbase.add_resource(opts.map_resource, nlmsa)
if opts.bind_attribute:
print '# saving worldbase schema with bindAttrs=(%s)' % opts.bind_attribute
genome_annotDB_relation = metabase.ManyToManyRelation(genome, annotDB, bindAttrs=(opts.bind_attribute,))
genome_annotDB_relation.__doc__ = 'GFF based mapping from %s to genome %s' % (opts.annotationDB_resource,
opts.genome_resource)
worldbase.add_schema('%s' % opts.map_resource, genome_annotDB_relation)
print '# committing worldbase resources'
worldbase.commit()
if __name__ == "__main__":
main()
def main():
"""Build an annotation from the given gff file
"""
usage = """Build and save the annotations defined in the given gff files
Saves an annotationDB (representing the file itself) and creates a mapping
in the form genome[chromosome][100:200].officialGenes"""
parser = optparse.OptionParser("%prog [options] data1.gff [data2.gff ...]\n"+usage)
parser.add_option("--genome_resource", '-g', dest="genome_resource", type="string",
help="""The pygr resource for the genome, eg, 'Bio.Seq.Genome.TRICA.triCas3'""")
parser.add_option("--annotationDB_resource", '-a', dest="annotationDB_resource", type="string",
help="""Where to save the created annotationDB. eg,
Bio.Annotation.TRICA.triCas3.officialGenes""")
parser.add_option("--save_pathstem", '-p', dest="pathstem", type="string",
help="""The file to save the exon resource to, eg,
'/home/baldig/projects/genomics/pygrdata/annotations/fly/triCas3_official_genes'""")
parser.add_option("--map_resource", '-m', dest="map_resource", type="string",
help="""the resource to save the annotationDB->Genome map,
saved both to worldbase and to worldbase.schema, eg,
'Bio.Annotation.TRICA.triCas3.BeetleBase.officialGenesMap""")
parser.add_option("--bind_attribute", '-b', dest="bind_attribute", type="string",
help="""The attribute to access annotationDB from genome region, eg,
'officialGenes' would be accessible via triCas3['ChLG2'][100:200].officialGenes
Default is not to bind an attribute to genome""")
(opts, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
print 'Please specify at least one gff file to read'
sys.exit(-1)
if None in [opts.genome_resource, opts.annotationDB_resource, opts.pathstem, opts.map_resource]:
parser.print_help()
print 'Required options: genome_resource, annotationDB_resource, pathstem, map_resource'
sys.exit(-1)
print '# Loading original genome db'
genome = worldbase(opts.genome_resource)
annotDB = annotation.AnnotationDB(None, genome, opts.bind_attribute,
filename=opts.pathstem + '_annotDB', mode='c', verbose=False)
nlmsa = cnestedlist.NLMSA(opts.pathstem, 'w', pairwiseMode=True, bidirectional=False)
index = 0 # unique ID used in annotationD
for filename in args:
print '# adding to annotationDB from %s' % filename
fileIn = open(filename)
for row in read_for_pygr(fileIn):
curAnnot = annotDB.new_annotation(index, row)
nlmsa.addAnnotation(curAnnot)
index += 1
annotDB.close() # Flush annotation data to disk
print '# building NLMSA from all gff files'
nlmsa.build(saveSeqDict=True)
print '# saving annotationDB and NLMSA to worldbase as %s and %s' % (opts.annotationDB_resource,
opts.map_resource)
annotDB.__doc__ = 'Combined gff annotationDB from files %s on genome %s' % (', '.join(args),
opts.genome_resource)
nlmsa.__doc__ = 'Mapping of %s, from gff files %s onto genome %s' % (opts.annotationDB_resource,
', '.join(args),
opts.genome_resource)
worldbase.add_resource(opts.annotationDB_resource, annotDB)
worldbase.add_resource(opts.map_resource, nlmsa)
if opts.bind_attribute:
print '# saving worldbase schema with bindAttrs=(%s)' % opts.bind_attribute
genome_annotDB_relation = metabase.ManyToManyRelation(genome, annotDB, bindAttrs=(opts.bind_attribute,))
genome_annotDB_relation.__doc__ = 'GFF based mapping from %s to genome %s' % (opts.annotationDB_resource,
opts.genome_resource)
worldbase.add_schema('%s' % opts.map_resource, genome_annotDB_relation)
print '# committing worldbase resources'
worldbase.commit()
