def initiate_case(batchSize):
reference = decoder("data/KR233687.fasta")
sequence = decoder("data/ERR1293055_first100.fastq")
refKmer = kmer_maker(13, reference, True)
seqKmer = kmer_maker(13, sequence, False)
reference_trie = Trie()
sternum = mapper(refKmer, seqKmer, reference_trie, batchSize)
sternum.filter_matching()
return sternum
def run():
reference = decoder(args.reference)
sequence = decoder(args.sequence)
if int(args.method) == 3:
spine = BWT(reference)
refKmer = reference
else:
refKmer = kmer_maker(int(args.ksize), reference, True)
seqKmer = kmer_maker(int(args.ksize), sequence, False)
if int(args.method) == 1: # mapping through Suffix Trie
spine = Trie()
elif int(args.method) == 2: # mapping through Suffix Array
spine = SA(reference)
sternum = mapper(refKmer, seqKmer, spine, int(args.batchSize))
sternum.filter_matching(int(args.minKcount), int(args.minPercentage))
reporter(sternum, args.outputPrefix + "_" + str(args.method) + "_")
def test_zclear(self):
"""
Test deleting kmers' files from disk
"""
fileName = "data/ERR1293055_first100.fastq"
fastaFile = decoder(fileName)
kmer = kmer_maker(13, fastaFile, False)
kmer.dump()
kmer.clear()
files = glob.glob(kmer.filePrefix + "_*" + kmer.fileExten)
self.assertEqual(dict(), kmer.kmers)
self.assertEqual(files, [])
def test_splice_fasta_overlapping(self):
"""
Test splicing fasta overlapping kmers
"""
fileName = "data/KR233687.fasta"
fastaFile = decoder(fileName)
kmer = kmer_maker(13, fastaFile, True)
self.assertIn(["GAGATCTAATGTC", 0], kmer.kmers["KR233687.2.1"])
self.assertIn(["TAATGGTGGCATA", 579], kmer.kmers["KR233687.2.1"])
self.assertIn(["ATTCAGTTGATAG", 1], kmer.kmers["KR233687.2.2"])
self.assertIn(["ATGGTCATCAATT", 1123], kmer.kmers["KR233687.2.2"])
self.assertEqual(2, kmer.seqCount)
def test_dump(self):
"""
Test storing kmers to disk
"""
fileName = "data/ERR1293055_first100.fastq"
fastaFile = decoder(fileName)
kmer = kmer_maker(13, fastaFile, False)
kmer.dump()
file = open("_39_ERR1293055.40.kmers")
lines = file.read()
self.assertIn("GTTGGGATCAATA", lines)
file.close()
def test_splice_fastq_Nonoverlapping(self):
"""
Test splicing fastq nonoverlapping kmers
"""
fileName = "data/ERR1293055_first100.fastq"
fastaFile = decoder(fileName)
kmer = kmer_maker(13, fastaFile, False)
self.assertIn(["CTCTTCTACTTCT", 0], kmer.kmers["ERR1293055.1"])
self.assertIn(["GTTGGGATCAATA", 0], kmer.kmers["ERR1293055.40"])
self.assertIn(["ATTCAAATGTTCC", 286], kmer.kmers["ERR1293055.100"])
self.assertNotIn("TCCACTTCACTTT", kmer.kmers["ERR1293055.90"])
self.assertEqual(100, kmer.seqCount)
def test_splice_fasta_Nonoverlapping(self):
"""
Test splicing fasta nonoverlapping kmers
"""
fileName = "data/KR233687.fasta"
fastaFile = decoder(fileName)
kmer = kmer_maker(13, fastaFile, False)
self.assertIn(["GAGATCTAATGTC", 0], kmer.kmers["KR233687.2.1"])
self.assertIn(["TCAATCCCGCACT", 13], kmer.kmers["KR233687.2.1"])
self.assertIn(["TTCGGATGGTCAT", 1118], kmer.kmers["KR233687.2.2"])
self.assertNotIn(["AGATCTAATGTCT", 1], kmer.kmers["KR233687.2.1"])
self.assertEqual(2, kmer.seqCount)
def test_load(self):
"""
Test storing kmers to disk
"""
fileName = "data/ERR1293055_first100.fastq"
fastaFile = decoder(fileName)
kmer = kmer_maker(13, fastaFile, False)
kmer.dump()
kmer.load("", 3)
self.assertIn("ERR1293055.3", kmer.kmers)
kmer.dump()
kmer.load("", 4)
self.assertIn("ERR1293055.7", kmer.kmers)
kmer.load("", -1)
self.assertIn("ERR1293055.100", kmer.kmers)