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reformat: The flag -T/--trim also does not add prefix for missing ran…
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…k lower than current rank. #82
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shenwei356 committed Jul 11, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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- [TaxonKit v0.14.3](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.3)
[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.3/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.3)
- `taxonkit reformat`:
- The flag `-T/--trim` also does not add prefix for missing rank lower than current rank. [#82](https://github.com/shenwei356/taxonkit/issues/82)
- [TaxonKit v0.14.2](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.2)
[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.2/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.2)
- `taxonkit filter`:
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120 changes: 95 additions & 25 deletions doc/docs/usage.md
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Expand Up @@ -122,7 +122,8 @@ Flags:
-h, --help help for list
-i, --ids string TaxId(s), multiple values should be separated by comma
-I, --indent string indent (default " ")
-J, --json output in JSON format. you can save the result in file with suffix ".json" and open with modern text editor
-J, --json output in JSON format. you can save the result in file with suffix ".json" and
open with modern text editor
-n, --show-name output scientific name
-r, --show-rank output rank
Expand Down Expand Up @@ -376,6 +377,55 @@ Examples
92489 cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae
1458427 cellular organisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raicheisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei


# wrapped table with csvtk pretty (>v0.26.0)
$ taxonkit lineage taxids.txt | csvtk pretty -Ht -x ';' -W 70 -S bold
┏━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ 9606 ┃ cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria; ┃
┃ ┃ Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi; ┃
┃ ┃ Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota; ┃
┃ ┃ Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates; ┃
┃ ┃ Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae; ┃
┃ ┃ Homo;Homo sapiens ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 9913 ┃ cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria; ┃
┃ ┃ Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi; ┃
┃ ┃ Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota; ┃
┃ ┃ Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla; ┃
┃ ┃ Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bos taurus ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 376619 ┃ cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria; ┃
┃ ┃ Thiotrichales;Francisellaceae;Francisella;Francisella tularensis; ┃
┃ ┃ Francisella tularensis subsp. holarctica; ┃
┃ ┃ Francisella tularensis subsp. holarctica LVS ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 349741 ┃ cellular organisms;Bacteria;PVC group;Verrucomicrobia; ┃
┃ ┃ Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia; ┃
┃ ┃ Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 239935 ┃ cellular organisms;Bacteria;PVC group;Verrucomicrobia; ┃
┃ ┃ Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia; ┃
┃ ┃ Akkermansia muciniphila ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 314101 ┃ cellular organisms;Bacteria;environmental samples; ┃
┃ ┃ uncultured murine large bowel bacterium BAC 54B ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 11932 ┃ Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes; ┃
┃ ┃ Ortervirales;Retroviridae;unclassified Retroviridae; ┃
┃ ┃ Intracisternal A-particles;Mouse Intracisternal A-particle ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 1327037 ┃ Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes; ┃
┃ ┃ Caudovirales;Siphoviridae;unclassified Siphoviridae; ┃
┃ ┃ Croceibacter phage P2559Y ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 92489 ┃ cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria; ┃
┃ ┃ Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae ┃
┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫
┃ 1458427 ┃ cellular organisms;Bacteria;Proteobacteria;Betaproteobacteria; ┃
┃ ┃ Burkholderiales;Comamonadaceae;Serpentinomonas; ┃
┃ ┃ Serpentinomonas raichei ┃
┗━━━━━━━━━┻━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛

1. Speed.

$ time echo 9606 | taxonkit lineage
Expand Down Expand Up @@ -530,10 +580,10 @@ Output:
1. Input line data.
2. Reformated lineage.
3. (Optional) TaxIds taxons in the lineage (-t/--show-lineage-taxids)
Ambiguous names:
- Some TaxIds have the same complete lineage, empty result is returned
- Some TaxIds have the same complete lineage, empty result is returned
by default. You can use the flag -a/--output-ambiguous-result to
return one possible result
Expand All @@ -548,46 +598,60 @@ Output format can be formated by flag --format, available placeholders:
{g}: genus
{s}: species
{t}: subspecies/strain
{S}: subspecies
{T}: strain
When these are no nodes of rank "subspecies" nor "strain",
When these're no nodes of rank "subspecies" nor "strain",
you can switch on -S/--pseudo-strain to use the node with lowest rank
as subspecies/strain name, if which rank is lower than "species".
as subspecies/strain name, if which rank is lower than "species".
This flag affects {t}, {S}, {T}.
Output format can contains some escape charactors like "\t".
Usage:
taxonkit reformat [flags]
Flags:
-P, --add-prefix add prefixes for all ranks, single prefix for a rank is defined by flag --prefix-X
-P, --add-prefix add prefixes for all ranks, single prefix for a rank is defined
by flag --prefix-X
-d, --delimiter string field delimiter in input lineage (default ";")
-F, --fill-miss-rank fill missing rank with lineage information of the next higher rank
-f, --format string output format, placeholders of rank are needed (default "{k};{p};{c};{o};{f};{g};{s}")
-f, --format string output format, placeholders of rank are needed (default
"{k};{p};{c};{o};{f};{g};{s}")
-h, --help help for reformat
-i, --lineage-field int field index of lineage. data should be tab-separated (default 2)
-r, --miss-rank-repl string replacement string for missing rank
-p, --miss-rank-repl-prefix string prefix for estimated taxon level (default "unclassified ")
-R, --miss-taxid-repl string replacement string for missing taxid
-a, --output-ambiguous-result output one of the ambigous result
--prefix-K string prefix for kingdom, used along with flag -P/--add-prefix (default "K__")
--prefix-S string prefix for subspecies, used along with flag -P/--add-prefix (default "S__")
--prefix-T string prefix for strain, used along with flag -P/--add-prefix (default "T__")
--prefix-K string prefix for kingdom, used along with flag -P/--add-prefix (default
"K__")
--prefix-S string prefix for subspecies, used along with flag -P/--add-prefix
(default "S__")
--prefix-T string prefix for strain, used along with flag -P/--add-prefix (default
"T__")
--prefix-c string prefix for class, used along with flag -P/--add-prefix (default "c__")
--prefix-f string prefix for family, used along with flag -P/--add-prefix (default "f__")
--prefix-f string prefix for family, used along with flag -P/--add-prefix (default
"f__")
--prefix-g string prefix for genus, used along with flag -P/--add-prefix (default "g__")
--prefix-k string prefix for superkingdom, used along with flag -P/--add-prefix (default "k__")
--prefix-k string prefix for superkingdom, used along with flag -P/--add-prefix
(default "k__")
--prefix-o string prefix for order, used along with flag -P/--add-prefix (default "o__")
--prefix-p string prefix for phylum, used along with flag -P/--add-prefix (default "p__")
--prefix-s string prefix for species, used along with flag -P/--add-prefix (default "s__")
--prefix-t string prefix for subspecies/strain, used along with flag -P/--add-prefix (default "t__")
-S, --pseudo-strain use the node with lowest rank as strain name, only if which rank is lower than "species" and not "subpecies" nor "strain". It affects {t}, {S}, {T}. This flag needs flag -F
--prefix-p string prefix for phylum, used along with flag -P/--add-prefix (default
"p__")
--prefix-s string prefix for species, used along with flag -P/--add-prefix (default
"s__")
--prefix-t string prefix for subspecies/strain, used along with flag
-P/--add-prefix (default "t__")
-S, --pseudo-strain use the node with lowest rank as strain name, only if which rank
is lower than "species" and not "subpecies" nor "strain". It
affects {t}, {S}, {T}. This flag needs flag -F
-t, --show-lineage-taxids show corresponding taxids of reformated lineage
-I, --taxid-field int field index of taxid. input data should be tab-separated. it overrides -i/--lineage-field
-T, --trim do not fill missing rank lower than current rank
-I, --taxid-field int field index of taxid. input data should be tab-separated. it
overrides -i/--lineage-field
-T, --trim do not fill or add prefix for missing rank lower than current rank
```

Expand Down Expand Up @@ -1044,15 +1108,19 @@ Flags:
-B, --black-list strings black list of ranks to discard, e.g., '-B "no rank" -B "clade"
-N, --discard-noranks discard all ranks without order, type "taxonkit filter --help" for details
-R, --discard-root discard root taxid, defined by --root-taxid
-E, --equal-to strings output TaxIds with rank equal to some ranks, multiple values can be separated with comma "," (e.g., -E "genus,species"), or give multiple times (e.g., -E genus -E species)
-E, --equal-to strings output TaxIds with rank equal to some ranks, multiple values can be
separated with comma "," (e.g., -E "genus,species"), or give multiple
times (e.g., -E genus -E species)
-h, --help help for filter
-H, --higher-than string output TaxIds with rank higher than a rank, exclusive with --lower-than
--list-order list user defined ranks in order, from "$HOME/.taxonkit/ranks.txt"
--list-ranks list ordered ranks in taxonomy database, sorted in user defined order
-L, --lower-than string output TaxIds with rank lower than a rank, exclusive with --higher-than
-r, --rank-file string user-defined ordered taxonomic ranks, type "taxonkit filter --help" for details
-r, --rank-file string user-defined ordered taxonomic ranks, type "taxonkit filter --help"
for details
--root-taxid uint32 root taxid (default 1)
-n, --save-predictable-norank do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff
-n, --save-predictable-norank do not discard some special ranks without order when using -L, where
rank of the closest higher node is still lower than rank cutoff
-i, --taxid-field int field index of taxid. input data should be tab-separated (default 1)
```
Expand Down Expand Up @@ -1726,7 +1794,8 @@ Flags:
-p, --percentage abundance is in percentage
-R, --recompute-abd recompute abundance if some TaxIds are deleted in current taxonomy version
-s, --sample-id string sample ID in result file
-r, --show-rank strings only show TaxIds and names of these ranks (default [superkingdom,phylum,class,order,family,genus,species,strain])
-r, --show-rank strings only show TaxIds and names of these ranks (default
[superkingdom,phylum,class,order,family,genus,species,strain])
-i, --taxid-field int field index of taxid. input data should be tab-separated (default 1)
-t, --taxonomy-id string taxonomy ID in result file
Expand Down Expand Up @@ -1836,7 +1905,8 @@ Flags:
--field-taxpathsn int field index of TAXPATHSN (default 4)
-h, --help help for cami-filter
--leaf-ranks strings only consider leaves at these ranks (default [species,strain,no rank])
--show-rank strings only show TaxIds and names of these ranks (default [superkingdom,phylum,class,order,family,genus,species,strain])
--show-rank strings only show TaxIds and names of these ranks (default
[superkingdom,phylum,class,order,family,genus,species,strain])
--taxid-sep string separator of taxid in TAXPATH and TAXPATHSN (default "|")
-t, --taxids strings the parent taxid(s) to filter out
-f, --taxids-file strings file(s) for the parent taxid(s) to filter out, one taxid per line
Expand Down
8 changes: 6 additions & 2 deletions taxonkit/cmd/reformat.go
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Original file line number Diff line number Diff line change
Expand Up @@ -490,7 +490,11 @@ Output format can contains some escape charactors like "\t".

for srank, re := range reRankPlaceHolders {
if addPrefix {
flineage = re.ReplaceAllString(flineage, prefixes[srank]+replacements[srank])
if trim && replacements[srank] == "" {
flineage = re.ReplaceAllString(flineage, "")
} else {
flineage = re.ReplaceAllString(flineage, prefixes[srank]+replacements[srank])
}
} else {
flineage = re.ReplaceAllString(flineage, replacements[srank])
}
Expand Down Expand Up @@ -570,5 +574,5 @@ func init() {
flineageCmd.Flags().StringP("prefix-S", "", "S__", `prefix for subspecies, used along with flag -P/--add-prefix`)
flineageCmd.Flags().StringP("prefix-T", "", "T__", `prefix for strain, used along with flag -P/--add-prefix`)

flineageCmd.Flags().BoolP("trim", "T", false, "do not fill missing rank lower than current rank")
flineageCmd.Flags().BoolP("trim", "T", false, "do not fill or add prefix for missing rank lower than current rank")
}
2 changes: 1 addition & 1 deletion taxonkit/cmd/version.go
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ import (
)

// VERSION of taxonkit
const VERSION = "0.14.2"
const VERSION = "0.14.3"

// versionCmd represents the version command
var versionCmd = &cobra.Command{
Expand Down

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