JoshuaTree2.py
def generate_synteny_structure(self,synteny_path):
        """Take anchor file or synteny file and searches for starting and ending genes for each syntenic block"""
        if self.synteny_file.endswith('.unout'):
            self.unout2structure(self.q_genome, self.s_genome)
        elif self.synteny_file.endswith('.lifted.anchors'):
            self.anchor2structure(self.q_genome, self.s_genome)
        elif self.synteny_file.endswith('.bed'):
            self.import_synteny_structure()
        else:
            self.run_synteny(self.q_genome,self.s_genome,synteny_path)
            self.anchor2structure(self.q_genome, self.s_genome)
        self.synteny_structure_index()
Take anchor file or synteny file and searches for starting and ending genes for each syntenic block
Take anchor file or synteny file and searches for starting and ending genes for each syntenic block
Take anchor file or synteny file and searches for starting and ending genes for each syntenic block
def generate_synteny_structure(self,synteny_path):
        if self.synteny_file.endswith('.unout'):
            self.unout2structure(self.q_genome, self.s_genome)
        elif self.synteny_file.endswith('.lifted.anchors'):
            self.anchor2structure(self.q_genome, self.s_genome)
        elif self.synteny_file.endswith('.bed'):
            self.import_synteny_structure()
        else:
            self.run_synteny(self.q_genome,self.s_genome,synteny_path)
            self.anchor2structure(self.q_genome, self.s_genome)
        self.synteny_structure_index()
def generate_synteny_structure ( self , synteny_path ) : if self . synteny_file . endswith ( '.unout' ) : self . unout2structure ( self . q_genome , self . s_genome ) elif self . synteny_file . endswith ( '.lifted.anchors' ) : self . anchor2structure ( self . q_genome , self . s_genome ) elif self . synteny_file . endswith ( '.bed' ) : self . import_synteny_structure ( ) else : self . run_synteny ( self . q_genome , self . s_genome , synteny_path ) self . anchor2structure ( self . q_genome , self . s_genome ) self . synteny_structure_index ( )
Take anchor file or synteny file and searches for starting and ending genes for each syntenic block
Take anchor file or synteny file and searches for starting and ending genes for each syntenic block
"""Take anchor file or synteny file and searches for starting and ending genes for each syntenic block"""
self
synteny_path