taxonomy find_diag_hits.py $input1 $id_col $rank_list $out_format $out_file1 Superkingdom Kingdom Subkingdom Superphylum Phylum Subphylum Superclass Class Subclass Superorder Order Suborder Superfamily Family Subfamily Tribe Subtribe Genus Subgenus Species Subspecies Diagnostic read list Number of diagnostic reads per taxonomic rank

**What it does** When performing metagenomic analyses it is often necessary to identify sequence reads corresponding to a particular taxonomic group, or, in other words, diagnostic of a particular taxonomic rank. This utility performs this analysis. It takes data generated by *Taxonomy manipulation->Fetch Taxonomic Ranks* as input and outputs either a list of sequence reads unique to a particular taxonomic rank, or a list of taxonomic ranks and the count of unique reads corresponding to each rank. ------ **Example** Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation:: read1 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n read2 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n read1 58615 root Eukaryota Metazoa n n Arthropoda n Hexapoda Insecta Neoptera Amphiesmenoptera Lepidoptera Glossata Papilionoidea Nymphalidae Nymphalinae Melitaeini Phyciodina Anthanassa n Anthanassa otanes n read3 56785 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n Running this tool with the following parameters: * *Select column with sequence id* set to **c1** * *Select taxonomic ranks* with **order**, and **genus** checked * *Output format* set to **Diagnostic read list** will return:: read2 Primates order read3 Primates order read2 Homo genus read3 Homo genus Changing *Output format* set to **Number of diagnostic reads per taxonomic rank** will produce:: Primates 2 order Homo 2 genus .. class:: infomark Note that **read1** is omitted because it is non-unique: it hits Mammals and Insects at the same time. -------- .. class:: warningmark This tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not.