create a method to automatically align HMW with batnames about hmw

[jhpoelen]

see related globalbioticinteractions/nomer#90 .

[jhpoelen]

@ajacsherman

with a first pass at Nomer's support for batnames (see globalbioticinteractions/nomer#91), you can now align hmw with batnames in less than 2 seconds:

$ time cat hmw.json | grep Chiroptera | jq --raw-output .name | sed 's/^/\t/g' | nomer append --include-header batnames | mlr --itsvlite --ocsv cat > hmw-batbase.csv
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [batnames]

real	0m1.595s
user	0m4.082s
sys	0m0.228s

See attached hmw-batnames.csv
hmw-batnames.csv

[jhpoelen]

There appear to be 131 names in HMW that are not included in the batnames. Note however, that the current support for batnames does not include synonym matching.

$ cat hmw-batnames.tsv | grep NONE | cut -f2

yields

Nycteris madagascariensis
Carollia brevicaudum
Anoura aequatoris
Anoura peruana
Lophostoma silvicola
Tonatia saurophila
Leptonyctenis curasoae
Mucronycteris schmidtorum
Lonchorhina fernandez
Artibeus gnomus
Platyriunus aquilus
Platyrrhinus chocoensis
Artibeus toltecus
Artibeus phaeotis
Artibeus watsoni
Artibeus rosenbergi
Artibeus glaucus
Artibeus bogotensis
Artibeus aztecus
Artibeus ravus
Artibeus cinereus
Artibeus anderseni
Chiroderma vizottoi
Platyrrhainus brachycephalus
Chironax tumulus
Rousettus celebensis
Lissonycteris angolensis
Doryrhina semoni
Doryrhina muscinus
Doryrhina stenotis
Doryrhina wollastoni
Doryrhina edwardshilli
Doryrhina corynophyllus
Hipposideros pratti
Anthops omatus
Emballonura seni
Emballonura beccarli
Tadarida latouchet
Mops trevor
Chaerephon jobensis
Chaerephon nigeriae
Chaerephon major
Chaerephon tomensis
Chaerephon pumilus
Chaerephon russatus
Chaerephon pusillus
Chaerephon atsinanana
Chaerephon jobimena
Chaerephon bregullae
Chaerephon plicatus
Chaerephon johorensis
Chaerephon solomonis
Chaerephon bemmeleni
Chaerephon ansorgei
Chaerephon aloysiisabaudiae
Chaerephon gallagheri
Chaerephon chapini
Chaerephon bivittatus
Chaerephon leucogaster
Natalus lanatus
Chilonatalus tumaidifrons
Myotis browni
Myotis peninsularis
Myotis keenii
Myotis melanorhinus
Murina huttonii
Kerivoula malpasi
Kerivoula crypta
Plecotus christii
Rhogeessa gracilis
Rhogeessa alleni
Histiotus diaphanopterus
Histiotus humboldti
Histiotus velatus
Histiotus magellanicus
Histiotus laephotis
Histiotus alienus
Histiotus montanus
Histiotus macrotus
Glauconycteris poensts
Neoromicia helios
Neoromicia grandidieri
Neoromicia roseveari
Neoromicia isabella
Neoromicia rendalli
Neoromicia brunnea
Nycticeinops schlieffenii
Hypsugo bemainty
Hypsugo crassulus
Hypsugo anchieta
Neoromicia nanus
Neoromicia stanleyi
Neoromicia robertsi
Neoromicia matroka
Neoromicia capensis
Neoromicia malagasyensis
Hypsugo joffrei
Nyctophilus macrotis
Pipustrellus adamsi
Pipustrellus wattsi
Pipustrellus papuanus
Pipustrellus abramus
Puipustrellus raceyi
Pipustrellus aero
Pipustrellus rusticus
Pipustrellus hesperidus
Pipustrellus paterculus
Pipustrellus minahassae
Pipustrellus ceylonicus
Pipustrellus javanicus
Pipustrellus endoi
Pipustrellus sturdeei
Pipustrellus hanaki
Pipustrellus pipistrellus
Pipustrellus pygmaeus
Rhinolophus deckend
Rhinolophus alticolus
Rhinolophus gorongosae
Rhinolophus odami
Rhinolophus comutus
Rhinolophus achilles
Rhinolophus kahuzi
Rhinolophusarcuatus
Rhinolophus cognotus
Rhinolophus monticolus
Rhinolophus perniger
Miniopterus eschscholtzii
Miniopterus blepotis
Muniopterus mossambicus
Miniopterus arenarius
Genetta genetta

@ajacsherman are these results expected?

[jhpoelen]

With this, you can also do alignments with other name lists, like @n8upham 's https://mammaldiversity.org@Nathan Upham (mammaldiversity.org) Please note you can now also make quick comparisons between MDD and batnames -

$ curl "https://raw.githubusercontent.com/mammaldiversity/mammaldiversity.github.io/master/_data/mdd.csv" | mlr --csv filter '$order == "CHIROPTERA"' | mlr --csv cut -f sciName | sed 's/_/ /g' | sed 's/^/\t/g' | nomer append batnames | grep NONE | head 
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 5670k  100 5670k    0     0  17.8M      0 --:--:-- --:--:-- --:--:-- 17.8M
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [batnames]
	sciName	NONE		sciName						
	Chironax tumulus	NONE		Chironax tumulus		
	Lissonycteris angolensis	NONE		Lissonycteris angolensis
	Coelops hirsutus	NONE		Coelops hirsutus		
	Doryrhina corynophyllus	NONE		Doryrhina corynophyllus		
	Doryrhina edwardshilli	NONE		Doryrhina edwardshilli		
	Doryrhina muscinus	NONE		Doryrhina muscinus		
	Doryrhina semoni	NONE		Doryrhina semoni		
	Doryrhina stenotis	NONE		Doryrhina stenotis		
	Doryrhina wollastoni	NONE		Doryrhina wollastoni		

61 names are defined in MDD that are not accepted in batnames.

according to

$ curl "https://raw.githubusercontent.com/mammaldiversity/mammaldiversity.github.io/master/_data/mdd.csv" | mlr --csv filter '$order == "CHIROPTERA"' | mlr --csv cut -f sciName | sed 's/_/ /g' | sed 's/^/\t/g' | tail -n+2 | nomer append batnames | grep NONE | wc -l
61