def setUp(self):
self.root = os.environ['BACFINDER_HOME']
self.exampledir = "%s/example/Streptococcus_pyogenes"%self.root
self.bacdir = "%s/bacteriocins"%self.root
self.genome_files = test_modules.getFNA(self.exampledir)
self.bacteriocins = "%s/bagel.fa"%self.bacdir
self.intergenes = "test_intergenes.fa"
self.annotated_genes = "test_genes.fa"
self.intermediate = "intermediate"
#self.training_labels = "%s/data/training/training.txt"%self.root
self.trainDir = "%s/data/training/protein"%self.root
self.training_labels = "%s/data/training/training_proteins4.txt"%self.root
if not os.path.exists(self.intermediate):
os.mkdir(self.intermediate)
self.bac_evalue = 0.000001
self.formatdb = True
self.bacteriocin_radius = 50000
self.verbose = True
self.keep_tmp = False
self.similarity = 0.65
self.numThreads = 1
self.output = "out"
self.keep_tmp = True
self.db = "testdb"
if os.path.exists(self.db):
os.remove(self.db)
self.fasta = "test.fa"
self.function_check = "correct_functions.txt"
def setUp(self):
self.root = os.environ['BACFINDER_HOME']
self.exampledir = "%s/example/Streptococcus_pyogenes"%self.root
self.bacdir = "%s/bacteriocins"%self.root
self.genome_files = test_modules.getFNA(self.exampledir)
self.six_frame_genome = "%s/example/all_orfs.fna"%self.root
self.six_frame_genome_index = "%s/example/all_orfs.fai"%self.root
self.bacteriocins = "%s/all_bacteriocins.fa"%self.bacdir
self.intergenes = "test_intergenes.fa"
self.annotated_genes = "test_genes.fa"
self.textdb = "%s/db/bacteria_database"%(self.root)
self.textpickle = "%s/db/bacteria_table.zip"%(self.root)
#self.intergenes = "%s/db/intergenes.txt"%(self.root)
#self.annotated_genes = "%s/db/annotated_genes.txt"%(self.root)
self.intermediate = "intermediate"
#self.training_labels = "%s/data/training/training.txt"%self.root
self.training_directory = "%s/data/training/protein"%self.root
self.training_labels = "%s/data/training/training_proteins.txt"%self.root
if not os.path.exists(self.intermediate):
os.mkdir(self.intermediate)
self.bac_evalue = 0.0001
self.formatdb = True
self.bacteriocin_radius = 25000
self.verbose = True
self.keep_tmp = False
self.similarity = 0.65
self.numThreads = 6
self.output = "out"
self.keep_tmp = True
self.proc = None
def setUp(self):
self.root = os.environ['BACFINDER_HOME']
self.exampledir = "%s/example/Streptococcus_pyogenes"%self.root
self.bacdir = "%s/bacteriocins"%self.root
self.annotated_genes = "test_genes.fa"
print "Example dir",self.exampledir
annotation.go(self.exampledir,self.annotated_genes,types=['.gbk'])
self.genome_files = test_modules.getFNA(self.exampledir)
self.bacteriocins = "%s/bagel.fa"%self.bacdir
self.genes = "%s/genes.fa"%self.bacdir
self.intergenes = "test_intergenes.fa"
intergene.go(self.exampledir,self.intergenes)
self.bacteriocinsOut = "test_out_bacteriocins.txt"
#self.filteredOut,
self.annotationsOut = "neighbor_genes.txt"
self.intermediate = "intermediate"
if not os.path.exists(self.intermediate):
os.mkdir(self.intermediate)
self.gene_evalue = 0.000001
self.bac_evalue = 0.000001
self.num_threads = 10
self.formatdb = True
#self.gene_radius = 50000
self.bacteriocin_radius = 50000
self.verbose = True
self.keep_tmp = False
def setUp(self):
self.root = "/home/nafizh/Boa_project/Boa"
self.exampledir = "%s/example/Streptococcus_pyogenes"%self.root
self.bacdir = "%s/bacteriocins"%self.root
self.genome_dir = test_modules.getFNA(self.exampledir)
self.bacteriocins = "%s/bagel.fa"%self.bacdir
self.intergenes = "%s/src/genome/test_intergenes.fa"%self.root #changed - Nafiz
self.annotated_genes = "%s/src/annotation/test_genes.fa"%self.root #changed - Nafiz
self.intermediate = "intermediate"
#self.training_labels = "%s/data/training/training.txt"%self.root
self.training_directory = "%s/data/training/protein"%self.root
self.training_labels = "%s/data/training/training_proteins.txt"%self.root
if not os.path.exists(self.intermediate):
os.mkdir(self.intermediate)
self.bac_evalue = 0.000001
self.formatdb = True
self.bacteriocin_radius = 50000
self.verbose = True
self.keep_tmp = False
self.similarity = 0.65
self.numThreads = 1
self.output = "out"
self.keep_tmp = True
def setUp(self):
self.root = "/home/nafizh/Boa_project/Boa" # changed by Nafiz
self.exampledir = "%s/example/Streptococcus_pyogenes"%self.root
self.bacdir = "%s/bacteriocins"%self.root
self.genome_files = test_modules.getFNA(self.exampledir)
# dont know about these two - Nafiz
self.six_frame_genome = "%s/example/all_orfs.fna"%self.root
self.six_frame_genome_index = "%s/example/all_orfs.fai"%self.root
self.bacteriocins = "%s/bacteriocins.fa"%self.bacdir #changed - Nafiz
self.intergenes = "%s/src/genome/test_intergenes.fa"%self.root #changed - Nafiz
self.annotated_genes = "%s/src/annotation/test_genes.fa"%self.root #changed - Nafiz
self.textdb = "%s/db/bacteria_database"%(self.root) #does not exist - dont know the usage - Nafiz
self.textpickle = "%s/db/bacteria_table.zip"%(self.root)
#self.intergenes = "%s/db/intergenes.txt"%(self.root)
#self.annotated_genes = "%s/db/annotated_genes.txt"%(self.root)
self.intermediate = "intermediate"
#self.training_labels = "%s/data/training/training.txt"%self.root
self.training_directory = "%s/data/training/protein"%self.root
self.training_labels = "%s/data/training/training_proteins.txt"%self.root
if not os.path.exists(self.intermediate):
os.mkdir(self.intermediate)
self.bac_evalue = 0.0001
self.formatdb = True
self.bacteriocin_radius = 25000
self.verbose = True
self.keep_tmp = False
self.similarity = 0.65
self.numThreads = 6
self.output = "out"
self.keep_tmp = True
self.proc = None
