ORFFinderInGraph.py 文件源码

def write_orfs(self, outdir):
        """
        Write ORFs from self.orfs and create files ORFs.[fasta, path] with sequences and paths
        :param outdir: saves path (with "/" in the end)
        """
        with open(outdir + 'ORFs.fasta', 'w') as f, open(outdir + 'ORFs.path', 'w') as path:
            counter = 0
            for o in self.orfs:
                SeqIO.write(SeqRecord(Seq(o), id='ORF_{0}'.format(counter), description=self.orfs[o][1]), f, 'fasta')
                path.write('ORF_{0} '.format(counter) + 'max_edge_len: {0}\n'.format(self.max_edge_len(o)) +
                           str(self.orfs[o][0][0]) + ',' + ''.join([i[0] + i[1] + ',' for i in self.orfs[o][0][1:-1]]) +
                           str(self.orfs[o][0][-1]) + '\n')
                counter += 1