def mis_rec_to_string(self, mis_rec):
     lvl = mis_rec['orig_level']
     output = mis_rec['name'] + "\t"
     output += "%s\t%s\t%s\t%.3f\t" % (mis_rec['level_name'], 
         mis_rec['orig_ranks'][lvl], mis_rec['ranks'][lvl], mis_rec['lws'][lvl])
     output += Taxonomy.lineage_str(mis_rec['orig_ranks']) + "\t"
     output += Taxonomy.lineage_str(mis_rec['ranks']) + "\t"
     output += ";".join(["%.3f" % conf for conf in mis_rec['lws']])
     if 'rank_conf' in mis_rec:
         output += "\t%.3f" % mis_rec['rank_conf']
     return output
Example #2
0
 def mis_rec_to_string(self, mis_rec):
     lvl = mis_rec['orig_level']
     uncorr_name = EpacConfig.strip_ref_prefix(self.refjson.get_uncorr_seqid(mis_rec['name']))
     uncorr_orig_ranks = self.refjson.get_uncorr_ranks(mis_rec['orig_ranks'])
     uncorr_ranks = self.refjson.get_uncorr_ranks(mis_rec['ranks'])
     output = uncorr_name + "\t"
   
     if lvl >= 0:
         output += "%s\t%s\t%s\t%.3f\t" % (mis_rec['level_name'], 
             uncorr_orig_ranks[lvl], uncorr_ranks[lvl], mis_rec['lws'][lvl])
     else:
         output += "%s\t%s\t%s\t%.3f\t" % (mis_rec['level_name'], 
             "NA", "NA", mis_rec['lws'][0])
     
     output += Taxonomy.lineage_str(uncorr_orig_ranks) + "\t"
     output += Taxonomy.lineage_str(uncorr_ranks) + "\t"
     output += ";".join(["%.3f" % conf for conf in mis_rec['lws']])
     if 'rank_conf' in mis_rec:
         output += "\t%.3f" % mis_rec['rank_conf']
     return output
Example #3
0
    def mis_rec_to_string(self, mis_rec):
        lvl = mis_rec['orig_level']
        uncorr_name = EpacConfig.strip_ref_prefix(
            self.refjson.get_uncorr_seqid(mis_rec['name']))
        uncorr_orig_ranks = self.refjson.get_uncorr_ranks(
            mis_rec['orig_ranks'])
        uncorr_ranks = self.refjson.get_uncorr_ranks(mis_rec['ranks'])
        output = uncorr_name + "\t"

        if lvl >= 0:
            output += "%s\t%s\t%s\t%.3f\t" % (
                mis_rec['level_name'], uncorr_orig_ranks[lvl],
                uncorr_ranks[lvl], mis_rec['lws'][lvl])
        else:
            output += "%s\t%s\t%s\t%.3f\t" % (mis_rec['level_name'], "NA",
                                              "NA", mis_rec['lws'][0])

        output += Taxonomy.lineage_str(uncorr_orig_ranks) + "\t"
        output += Taxonomy.lineage_str(uncorr_ranks) + "\t"
        output += ";".join(["%.3f" % conf for conf in mis_rec['lws']])
        if 'rank_conf' in mis_rec:
            output += "\t%.3f" % mis_rec['rank_conf']
        return output