Python mapping_container Examples

Example #1

File: tests.py Project: ctb/Caper

    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)

Example #2

File: tests.py Project: voidptr/Caper

 def setup(self):
     self.cont = caper.mapping_container(map_bundle)
     self.db = seqdb.SequenceFileDB(sequence_path)
     self.seq = self.db[contig]

Example #3

File: test_misc.py Project: ctb/Caper

 def setup(self):
     self.engine = caper.mapping_container(bundle_path)

Example #4

File: foo.py Project: ctb/Caper

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