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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -41,7 +41,7 @@ All-in-one command: | |
| ```text | ||
| TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit | ||
| Version: 0.14.0 | ||
| Version: 0.14.2 | ||
| Author: Wei Shen <[email protected]> | ||
|
|
@@ -58,13 +58,13 @@ Dataset: | |
| "/home/shenwei/.taxonkit" | ||
| or some other directory, and later you can refer to using flag --data-dir, | ||
| or environment variable TAXONKIT_DB | ||
| or environment variable TAXONKIT_DB. | ||
| When environment variable TAXONKIT_DB is set, explicitly setting --data-dir will | ||
| overide the value of TAXONKIT_DB. | ||
| Usage: | ||
| taxonkit [command] | ||
| taxonkit [command] | ||
| Available Commands: | ||
| cami-filter Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile | ||
|
|
@@ -83,7 +83,8 @@ Available Commands: | |
| Flags: | ||
| --data-dir string directory containing nodes.dmp and names.dmp (default "/home/shenwei/.taxonkit") | ||
| -h, --help help for taxonkit | ||
| --line-buffered use line buffering on output, i.e., immediately writing to stdin/file for every line of output | ||
| --line-buffered use line buffering on output, i.e., immediately writing to stdin/file for | ||
| every line of output | ||
| -o, --out-file string out file ("-" for stdout, suffix .gz for gzipped out) (default "-") | ||
| -j, --threads int number of CPUs. 4 is enough (default 4) | ||
| --verbose print verbose information | ||
|
|
@@ -1115,10 +1116,11 @@ Examples | |
| | csvtk pretty -H -t | ||
| 2 superkingdom Bacteria | ||
|
|
||
| 1. "no rank" and "clade" have no rank and can be filter out via `-N/--discard-noranks`. | ||
| Futher ranks can be removed with black list via `-B/--black-list` | ||
| 1. TaxIDs with no rank are kept by default!!! | ||
| "no rank" and "clade" have no rank and can be filter out via `-N/--discard-noranks`. | ||
| Futher ranks can be removed with black list via `-B/--black-list`. | ||
|
|
||
| # 562 is TaxId of Escherichia coli | ||
| # 562 is the TaxId of Escherichia coli | ||
| $ taxonkit list --ids 562 \ | ||
| | taxonkit filter -L species \ | ||
| | taxonkit lineage -r -n -L \ | ||
|
|
||
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