prophyle_assignment.py 文件源码

def print_sam_header(self):
        """Print SAM headers.
        """
        print("@HD", "VN:1.5", "SO:unsorted", sep="\t", file=self.output_fo)
        print("@PG", "PN:prophyle", "ID:prophyle", "VN:{}".format(version.VERSION), sep="\t", file=self.output_fo)
        for node in self.tree_index.tree.traverse("postorder"):

            try:
                ur = "\tUR:{}".format(node.fastapath)
            except:
                ur = ""

            try:
                sp = "\tSP:{}".format(node.sci_name)
            except:
                sp = ""

            try:
                as_ = "\tAS:{}".format(node.gi)
            except:
                as_ = ""

            if node.name != '':
                print(
                    "@SQ\tSN:{rname}\tLN:{rlen}{as_}{ur}{sp}".format(
                        rname=node.name,
                        rlen=CONFIG['FAKE_CONTIG_LENGTH'],
                        as_=as_,
                        ur=ur,
                        sp=sp,
                    ), file=self.output_fo
                )