Critical Element name and description
- Name of the element: "Classification Report"
- Description of the element on the Scene: "Generate a detailed classification report"
- Description of the element in the Property Editor:
"Based on the input taxonomy classification data the element generates a detailed report and saves it in a tab-delimited text format."
Input data
There is one input port:
| Item | Value |
|---|---|
| Port name in GUI | Input taxonomy data |
| Port description | Input taxonomy data from one of the classification elements (Kraken, CLARK, etc.). |
| Port ID in UWL | in |
| Number of slots | 1 |
| Slot #1 name in GUI | Input tax data |
| Slot #1 ID in UWL | tax_data |
| Slot #1 data type | Taxonomy classification |
Parameters
| # | Parameter | Description | Value in GUI | Default value |
|---|---|---|---|---|
| 1 | Output file | Specify the output text file name. | A line edit with the browse button. The value is mandatory ("Required"). | Auto (this equals to "input_file_name_report.txt" |
Data processing by the element
- The element takes input taxonomy classification data.
- It generated the following header line in the output text file:
tax_id\ttax_name\trank\tlineage\tkingdom_tax_id\tkingdom_name\tphylum_tax_id\tphylum_name\tclass_tax_id\tclass_name\torder_tax_id\torder_name\tfamily_tax_id\tfamily_name\tgenus_tax_id\tgenus_name\tspecies_tax_id\tspecies_name\tdirectly_num\tdirectly_proportion_all(%)\tdirectly_proportion_classified(%)\tclade_num\tclade_proportion_all(%)\tclade_proportion_classified(%)
- For each taxID it generates a tab-delimited line in a text file with the following columns:
- the read tax ID
- scientific name of this taxon
- rank of the tax ID (as in the NCBI taxonomy, including such values as "subspecies", "superorder", etc.)
- lineage, i.e. all parent taxa in semicolon-separated list (see CLARK "estimate_abundance" output)
- kingdom tax ID of the parent taxa at the kingdom level
- the corresponding kingdom scientific name
- ... (the same for all levels, "−" in case the info is not available)
- "directly_num", i.e. the number of reads, directly assigned to this taxon.
- proportion of the reads in all reads (percentage value)
- proportion in classified reads only
- "clade_num", i.e. the number of reads, covered by the clade rooted at this taxon (the reads directly assigned and all their children)
- proportion of reads, covered by the clade rooted at this taxon, in all reads
- proportion of reads, covered by the clade rooted at this taxon, in classified reads