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 lancer():
if var_demo.get() == 0:
if var_mode.get() == "encode":
if var_choix.get() == "fichier":
valeur = entre_file.get()
elif var_choix.get() == "texte":
valeur = var_texte.get()
encoder(var_choix.get(), valeur, var_save.get())
else:
valeur = entre_file.get()
if var_correc.get() == 0:
decoder(valeur, var_save.get(), True)
else:
print("sans correection")
decoder(valeur, var_save.get(), False)
else:
valeur = entre_texte_demo.get()
temps, s_bytes, s_trit1, len_Trit, nb0, s_trit3, s_trit4, s_dna, dicoDebut, dicoReverse, dicoI3, ID, dicoP, dicoIX, dicoIX_dna, dicoFinal, s_dna_final = encoder(
"texte", valeur, var_save.get())
var_afficher = afficherEncodage(valeur, temps, s_bytes, s_trit1,
len_Trit, nb0, s_trit3, s_trit4, s_dna,
dicoDebut, dicoReverse, dicoI3, ID,
dicoP, dicoIX, dicoIX_dna, dicoFinal,
s_dna_final)
fenetre_demo = Tk()
fenetre_demo.title(
"Démonstration de l'encodage d'un texte vers de l'ADN")
barre = Scrollbar(fenetre_demo)
label_demo = Text(fenetre_demo, yscrollcommand=barre.set)
barre.config(command=label_demo.yview)
barre.pack(side="right", fill='y')
label_demo.pack(expand=1, fill="both")
label_demo.insert(0.0, var_afficher)
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)
def test_fastq(self):
"""
Test if properly decoded
"""
fileName = "data/ERR1293055_first100.fastq"
fastaFile = decoder(fileName)
result = fastaFile.seq
expected = "CTCTTCTACTTCTACACCTAATACATCCCCTCCCTCCCTCTCCCCCCTCCCCCTTCCT"
self.assertIn(expected, str(result["ERR1293055.1"]))
expected = "CACCCTTTCTTTATCCTTTTTATTTCTAATCTTTTTTTGTCGTTTCGTCTTTTTTTTT"
self.assertIn(expected, str(result["ERR1293055.15"]))
expected = "ATACAAAGCAAATCAAGGCAAAATAATTGGCCGAACAGATGTTAGCTTTAGTGGAGGA"
self.assertIn(expected, str(result["ERR1293055.99"]))
def decodeall(self):
"""
Attempt to decode all documents and store them to mongo
"""
for entry in os.listdir(self.storedir):
full_path = os.path.join(self.storedir, entry)
if os.path.isfile(full_path) and entry[0] != '.':
try:
mydive = decoder(self.storedir, entry)
if mydive.verifydata():
mydive.decode()
# print(mydive.datadict)
if "profilenumber" in mydive.datadict:
hits = self.mongocollection.find({"profilenumber": mydive.datadict["profilenumber"]})
# print("Count at database ", hits.count())
if hits.count() == 0:
self.mongocollection.insert_one(mydive.datadict)
logger.debug('Saved %s to mongodb', mydive.datadict["profilenumber"])
except:
logger.debug('Error decoding %s', entry)
def test_fasta(self):
"""
Test if properly decoded
"""
fileName = "data/KR233687.fasta"
fastaFile = decoder(fileName)
result = fastaFile.seq
expected = "GAGATCTAATGTCTCAATCCCGCACTCGCGAGATACTAACAAAAACCACTGTGGACCA\
TATGGCCATAATCAAGAAATACACATCAGGAAGACAAGAGAAGAACCCTGCTCTCAGAATGAAATGGATGATGGCAAT\
GAAATATCCAATCACAGCAGACAAGAGAATAATGGAAATGATTCCTGAAAGAAATGAACAAGGCCAGACGCTTT\
GGAGCAAGACAAATGATGCTGGATCAGACAGAGTGATGGTGTCTCCCCTAGCTGTAACTTGGTGGAATAG"
self.assertIn(expected, result["KR233687.2.1"])
expected = "GGAGTGGAATCTGCAGTGCTGAGGGGGTTCCTAATTCTGGGCAGGGAGGACAGAAGA\
TATGGACCAGCACTAAGCATCAATGAACTGAGCAATCTTGCGAAAGGGGAGAAAGCCAATGTGCTGATAGGGCAAGG\
AGACGTGGTGCTGGTAATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATT\
CGGATGGTCATCAATT"
self.assertIn(expected, result["KR233687.2.2"])
t0 = datetime.now()
print('RUN_START: ' + str(t0))
N_tweets = 0
N_matches = 0
N_warnings = 0
N_errors = 0
N_duplicates = 0
N_large_duplicates = 0
for f in files:
if f[-5:] == '.json':
#try:
if int(f[:8]) >= int(start):
if int(f[:8]) <= int(end):
d = decoder(keywords, dirIn, dirOut, hiMem, mode, lcase, emoji,
logging, yesterday_dict, today_dict)
#record = d.fixjson(dirIn, f, hiMem, emojiFile)
record = d.fixjson(dirIn, f, hiMem)
if logging:
print('\n# FILE STATS #')
print('FILE: ' + str(f))
n_tweets = d.n_tweets
N_tweets += n_tweets
print('TWEETS: ' + str(n_tweets))
n_matches = d.n_matches
N_matches += n_matches
print('MATCHES: ' + str(n_matches))
n_warnings = d.n_warnings
N_warnings += n_warnings
print('WARNINGS: ' + str(n_warnings))
joindre_salon_nok={}
joindre_salon_nok["taille"]=125
joindre_salon_nok["seq"]=1
joindre_salon_nok["Type"]=12
ack={}
ack["taille"]=125
ack["seq"]=1
ack["Type"]=63
print("---------- TEST TYPE 1 ----------\n")
print(inscription)
test1=encode.encoder(inscription)
print("\n{0}\n".format(test1))
test1bis=decode.decoder(test1)
print(test1bis)
print("\n---------- TEST TYPE 2 ----------\n")
print(film)
test2=encode.encoder(film)
print("\n{0}\n".format(test2))
test2bis=decode.decoder(test2)
print(test2bis)
print("\n---------- TEST TYPE 3 ----------\n")
print(user)
test3=encode.encoder(user)
print("\n{0}\n".format(test3))
test3bis=decode.decoder(test3)
print(test3bis)
print("\n---------- TEST TYPE 4 ----------\n")
print(maj_user)
print("\n---------- TEST TYPE 9 ----------\n")
print(desinscription)
test9=encode.encoder(desinscription)
print("\n{0}\n".format(test9))
test9bis=decode2.decoder(test9)
print(test9bis)
print("\n---------- TEST TYPE 10 ----------\n")
print(redir)
test10=encode.encoder(redir)
print("\n{0}\n".format(test10))
test10bis=decode2.decoder(test10)
print(test10bis)
print("\n---------- TEST TYPE 11 ----------\n")
print(joindre_salon_ok)
test11=encode.encoder(joindre_salon_ok)
print("\n{0}\n".format(test11))
test11bis=decode.decoder(test11)
print(test11bis)
print("\n---------- TEST TYPE 12 ----------\n")
print(joindre_salon_nok)
test12=encode.encoder(joindre_salon_nok)
print("\n{0}\n".format(test12))
test12bis=decode.decoder(test12)
print(test12bis)
print("\n---------- TEST TYPE 13 ----------\n")
print(ack)
test13=encode.encoder(ack)
print("\n{0}\n".format(test13))
test13bis=decode.decoder(test13)
print(test13bis)
from decode import decoder
from encode import encoder
assert decoder(encoder("alodicksiano")) == "alodicksiano"
assert decoder(encoder("alodicksiano")) == "alodicksiano"
assert decoder(encoder("alodicksiano")) == "alodicksiano"
assert decoder(encoder("123456789 123456789 123456789 123456789")
) == "123456789 123456789 123456789 123456789"