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