Python BlastDatabase.formatDb示例

示例#1

文件： dbfasta.py 项目： numerodix/gridportal

	def formatDb(self):
		BlastDatabase.formatDb(self)
		invoke = ConfigSys.loadmpi + "; "
		invoke += ConfigSys.mpiformatdb + " -N " + str(self.segments)
		invoke += " --config-file " + self.conf_file
		invoke += " -i " + self.name
		if (self.flag_skipreorder):
			invoke += " --skip-reorder"
			
		# declare protein or nucleotide (not necessary to specify but why not)
		if self.protein:
			invoke += " -p T"
		else:
			invoke += " -p F"
			
		self.invokeCmd(invoke)
		
		self.resetDbFormatPath()

示例#2

文件： dbasn1.py 项目： numerodix/gridportal

	def formatDb(self):
		invoke = ""
		if (self.flag_skipreorder):
			invoke += self.getCombinedFormatString(self.name)
		else:
			self.dumpToFasta(self.name)
			invoke += self.getSingleFormatString(self.name)

		# declare protein or nucleotide
		# only necessary when piping from fastacmd to mpiformatdb, but
		# making it a general requirement for consistency
		if self.protein:
			invoke += " -p T"
		else:
			invoke += " -p F"

		BlastDatabase.formatDb(self)
		self.invokeCmd(invoke)
		
		self.resetDbFormatPath()