def buildGenomicFunctionalAnnotation(infiles, outfiles):
territories_gtf_file = infiles[0]
PipelineGeneset.buildGenomicFunctionalAnnotation(territories_gtf_file,
dbh=connect(),
outfiles=outfiles)
def annotateGenome(infile, outfile):
"""This task only considers protein coding genes as
processed_transcripts tend to cover larger genomic regions and
often overlap between adjacent protein coding genes.
"""
PipelineGeneset.annotateGenome(infile, outfile, only_proteincoding=True)
def buildGenomicFunctionalAnnotation(infiles, outfiles):
territories_gtf_file = infiles[0]
PipelineGeneset.buildGenomicFunctionalAnnotation(
territories_gtf_file,
dbh=connect(),
outfiles=outfiles,
job_memory=PARAMS["job_memory"])
def annotateGeneStructure(infile, outfile):
"""This task only considers protein coding genes as
processed_transcripts tend to cover larger genomic regions and
often overlap between adjacent protein coding genes.
"""
PipelineGeneset.annotateGeneStructure(infile,
outfile,
only_proteincoding=True,
job_memory=PARAMS["job_memory"])
def collectCpGIslands(infile, outfile):
'''select repeats from UCSC and write to *outfile* in gff format.
'''
dbhandle = PipelineGeneset.connectToUCSC()
# Repeats are either stored in a single ``rmsk`` table (hg19) or in
# individual ``rmsk`` tables (mm9) like chr1_rmsk, chr2_rmsk, ....
# In order to do a single statement, the ucsc mysql database is
# queried for tables that end in rmsk.
cc = dbhandle.cursor()
table = "cpgIslandExt"
sql = """SELECT chrom, chromStart, chromEnd, name, obsExp
FROM %(table)s
""" % locals()
E.debug("executing sql statement: %s" % sql)
cc.execute(sql)
outf = IOTools.openFile(outfile, "w")
for data in cc.fetchall():
outf.write("\t".join(map(str, data)) + "\n")
outf.close()
def collectCpGIslands(infile, outfile):
'''select repeats from UCSC and write to *outfile* in gff format.
'''
dbhandle = PipelineGeneset.connectToUCSC()
# Repeats are either stored in a single ``rmsk`` table (hg19) or in
# individual ``rmsk`` tables (mm9) like chr1_rmsk, chr2_rmsk, ....
# In order to do a single statement, the ucsc mysql database is
# queried for tables that end in rmsk.
cc = dbhandle.cursor()
table = "cpgIslandExt"
sql = """SELECT chrom, chromStart, chromEnd, name, obsExp
FROM %(table)s
""" % locals()
E.debug("executing sql statement: %s" % sql)
cc.execute(sql)
outf = IOTools.openFile(outfile, "w")
for data in cc.fetchall():
outf.write("\t".join(map(str, data)) + "\n")
outf.close()
def loadGeneSetGeneInformation(infile, outfile):
PipelineGeneset.loadGeneStats(infile, outfile)
def loadGeneSetGeneInformation(infile, outfile):
PipelineGeneset.loadGeneStats(infile, outfile)
