def setup(self):
try:
screed
except NameError:
raise SkipTest
self.cont = caper.mapping_container(map_bundle)
self.db = seqdb.SequenceFileDB(sequence_path) #ScreedSequenceDB('data/REL606.gmc.fa')
self.db = ScreedSequenceDB(sequence_path)
self.seq = self.db[contig]
self.reads_db = ScreedSequenceDB(sequence_fastq)
self.al = CaperBridge(self.cont, self.db, self.reads_db)
def setup(self):
self.cont = caper.mapping_container(map_bundle)
self.db = seqdb.SequenceFileDB(sequence_path)
self.seq = self.db[contig]
def setup(self):
self.engine = caper.mapping_container(bundle_path)
import caper
#bundle_path = '/scratch2/rose/capertestdata/out/s_1_sequence.map.trim3-20.bundle'
#contig = 'Contig0'
bundle_path = 'data/cache/REL606-maq-map.txt.bundle'
contig = 'rel606'
engine = caper.mapping_container(bundle_path)
print "ENGINE"
print "------"
print "GET READ LENGTH"
length = engine.get_read_length()
print length
print
print "GET READS"
reads = engine.get_reads(contig,13)
for item in reads:
print item
print
print "GET INTERSECT"
inte = engine.get_intersect(contig,4)
for item in inte:
for read in item[4]:
print read