update readme

README.md

@@ -20,6 +20,7 @@ to create NCBI-style taxdump files for any taxonomy dataset, including GTDB and
 * [Download](#download)
 * [Results](#results)
     + [Taxon history of *Escherichia coli*](#taxon-history-of-escherichia-coli)
+    + [Species of the genus *Escherichia*](#species-of-the-genus-escherichia)
     + [Common manipulations](#common-manipulations)
 * [Citation](#citation)
 * [Contributing](#contributing)
@@ -149,7 +150,8 @@ Frequency of species
     $ csvtk freq -t -nr -f species taxid.map.stats.tsv \
         > taxid.map.stats.freq-species.tsv
         
-    $ head -n 21 taxid.map.stats.freq-species.tsv | csvtk pretty -t
+    $ head -n 21 taxid.map.stats.freq-species.tsv \
+        | csvtk pretty -t
     species                      frequency
     --------------------------   ---------
     Escherichia coli             26859
@@ -256,6 +258,56 @@ also shows the taxonomic information of current version (R207) and the taxon his
 |R207   |d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli    |
 |R202   |d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia flexneri|
 
+### Species of the genus Escherichia
+
+    # set the direcotory of taxdump file
+    export TAXONKIT_DB=gtdb-taxdump/R207
+
+    $ taxonkit list --ids 3334977531 -I "" \
+        | taxonkit filter  -E species \
+        | taxonkit lineage -Lnr \
+        | tee Escherichia.tsv
+    205980079       Escherichia ruysiae     species
+    266095079       Escherichia marmotae    species
+    1474290498      Escherichia sp004211955 species
+    2519456452      Escherichia sp002965065 species
+    2673387089      Escherichia coli_E      species
+    2878517233      Escherichia albertii    species
+    3072179875      Escherichia fergusonii  species
+    3820717297      Escherichia sp005843885 species
+    4093283224      Escherichia coli        species
+    4221400829      Escherichia sp001660175 species
+
+    $ csvtk join -Ht Escherichia.tsv \
+        <(cut -f 1 Escherichia.tsv \
+            | rush 'echo -ne "{}\t$(taxonkit list --ids {} -I "" \
+            | taxonkit filter -L species | wc -l)\n"') \
+        | csvtk add-header -t -n "taxid,name,rank,#assembly" \
+        | csvtk sort -t -k "#assembly:nr" -k name \
+        | csvtk csv2md -t
+        
+|taxid     |name                   |rank   |#assembly|
+|:---------|:----------------------|:------|:--------|
+|4093283224|Escherichia coli       |species|26859    |
+|2878517233|Escherichia albertii   |species|107      |
+|266095079 |Escherichia marmotae   |species|82       |
+|3072179875|Escherichia fergusonii |species|77       |
+|3820717297|Escherichia sp005843885|species|37       |
+|205980079 |Escherichia ruysiae    |species|36       |
+|4221400829|Escherichia sp001660175|species|3        |
+|1474290498|Escherichia sp004211955|species|2        |
+|2673387089|Escherichia coli_E     |species|1        |
+|2519456452|Escherichia sp002965065|species|1        |
+
+What's the *Escherichia coli_E*? There's only one genome: [GCF_011881725.1](https://gtdb.ecogenomic.org/genome?gid=GCF_011881725.1)
+
+    $ taxonkit list --ids 2673387089 -nr 
+    2673387089 [species] Escherichia coli_E
+      1744010345 [no rank] 011881725
+
+    $ grep 1744010345 gtdb-taxdump/R207/taxid.map 
+    GCF_011881725.1 1744010345
+
 ### Common manipulations
 
 Except the four taxdump files, we provide a `taxid.map` file which maps genome accessions to TaxIds.

gtdb-taxdump/R207/ranks.txt

@@ -0,0 +1,107 @@
+
+# This file defines taxonomic rank order for taxdump/taxonkit.
+# 
+# Here'are the rules:
+#     1. Blank lines or lines starting with "#" are ignored.
+#     2. Ranks are in decending order and case ignored.
+#     3. Ranks with same order should be in one line separated with comma (",", no space).
+#     4. Ranks without order should be assigned a prefix symbol "!" for each rank.
+# 
+# Deault ranks reference from https://en.wikipedia.org/wiki/Taxonomic_rank ,
+# and contains some ranks from NCIB Taxonomy database.
+#
+
+!no rank
+!clade
+
+
+life
+
+domain,superkingdom,realm,empire
+
+kingdom
+subkingdom
+infrakingdom
+parvkingdom
+
+superphylum,superdivision
+phylum,division
+subphylum,subdivision
+infraphylum,infradivision
+microphylum,microdivision
+
+superclass
+class
+subclass
+infraclass
+parvclass
+
+superlegion
+legion
+sublegion
+infralegion
+
+supercohort
+cohort
+subcohort
+infracohort
+
+gigaorder
+magnorder,megaorder
+grandorder,capaxorder
+mirorder,hyperorder
+superorder
+# series
+order
+# parvorder
+nanorder
+hypoorder
+minorder
+suborder
+infraorder
+parvorder
+
+# section
+# subsection
+
+gigafamily
+megafamily
+grandfamily
+hyperfamily
+superfamily
+epifamily
+# series
+group
+family
+subfamily
+infrafamily
+
+supertribe
+tribe
+subtribe
+infratribe
+
+genus
+subgenus
+section
+subsection
+series
+subseries
+
+
+superspecies,species group
+species subgroup
+species
+
+subspecies,forma specialis,pathovar
+
+pathogroup,serogroup
+biotype,serotype,genotype
+
+variety,varietas,morph,aberration
+subvariety,subvarietas,submorph,subaberration
+form,forma
+subform,subforma
+
+strain
+isolate