diff options
Diffstat (limited to 'data_tol_old')
| -rwxr-xr-x | data_tol_old/genTestImgs.sh | 16 | ||||
| -rw-r--r-- | data_tol_old/tolData.txt | 388 | ||||
| -rwxr-xr-x | data_tol_old/txtTreeToJSON.py | 76 |
3 files changed, 0 insertions, 480 deletions
diff --git a/data_tol_old/genTestImgs.sh b/data_tol_old/genTestImgs.sh deleted file mode 100755 index 21b001b..0000000 --- a/data_tol_old/genTestImgs.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash -set -e - -#generate tol.json from tol.txt -cat tolData.txt | ./txtTreeToJSON.py > tolData.json - -#reads through tolData.json, gets names, and generates image for each name -cat tolData.json | \ - gawk 'match ($0, /"name"\s*:\s*"([^"]*)"/, arr) {print arr[1]}' | \ - while read; do - convert -size 200x200 xc:khaki +repage \ - -size 150x150 -fill black -background None \ - -font Ubuntu-Mono -gravity center caption:"$REPLY" +repage \ - -gravity Center -composite -strip ../public/img/"$REPLY".png - done - diff --git a/data_tol_old/tolData.txt b/data_tol_old/tolData.txt deleted file mode 100644 index f73a064..0000000 --- a/data_tol_old/tolData.txt +++ /dev/null @@ -1,388 +0,0 @@ -Tree of Life - Viruses - Caudovirales - Herpesvirales - Ligamenvirales - Mononegavirales - Nidovirales - Picornavirales - Tymovirales - Archaea - Crenarchaeota - Euryarchaeota - Bacteria - Acidobacteria - Actinobacteria - Aquificae - Armatimonadetes - Bacteroidetes - Caldiserica - Chlamydiae - Chlorobi - Chloroflexi - Chrysiogenetes - Cyanobacteria - Deferribacteres - Deinococcus-thermus - Dictyoglomi - Elusimicrobia - Fibrobacteres - Firmicutes - Fusobacteria - Gemmatimonadetes - Lentisphaerae - Nitrospira - Planctomycetes - Proteobacteria - Spirochaetae - Synergistetes - Tenericutes - Thermodesulfobacteria - Thermotogae - Verrucomicrobia - Eukaryota - Diatoms - Amoebozoa - Plantae - Rhodopyhta - Viridiplantae - Prasinophytes - Ulvophyceae - Streptophyta - Charales - Embryophytes - Marchantiomorpha - Anthocerotophyta - Bryophyta - Lycopodiopsida - Lycopodiidae - Selaginellales - Polypodiopsida - Polypodiidae - Polypodiales - Equisetidae - Spermatopsida - Cycads - Conifers - Taxaceae - Cupressaceae - Pinaceae - Pinus - Picea - Larix - Cedrus - Abies - Ginkgos - Angiosperms - Illicium - magnoliids - Piperales - Piperaceae - Magnoliales - Annonaceae - Myristicaceae - Laurales - Lauraceae - Monocotyledons - Alismatanae - Aranae - Liliaceae - Asparagales - Amaryllidaceae - Asparagaceae - Asphodelaceae - Iridaceae - Orchidaceae - Dioscoreaceae - Arecanae - Cocoeae - Phoeniceae - Zingiberanae - Musaceae - Strelitziaceae - Zingiberaceae - Commelinanae - Bromeliaceae - Cyperaceae - Typhaceae - Poaceae - Zea mays - Triticum - Bambusoideae - eudicots - Ranunculales - Papaveraceae - Ranunculaceae - Proteales - Proteaceae - Nelumbo - Core Eudicots - Saxifragales - Rosids - Fabaceae - Mimosoideae - IRLC (Inverted Repat-lacking clade) - Trifolieae - Fabeae - Rosales - Rosaceae - Rosa - Malus pumila - Ulmaceae - Urticaceae - Moraceae - Cannabaceae - Fagales - Fagaceae - Betulaceae - Juglandaceae - Cucurbitales - Cucurbitaceae - Malpighiales - Salicaceae - Violaceae - Passifloraceae - Erythroxylaceae - Rhizophoraceae - Euphorbiaceae - Linaceae - Rafflesiaceae - Myrtales - Myrtaceae - Onagraceae - Lythraceae - Brassicales - Caricaceae - Brassicaceae - Malvales - Core Malvales - Malvoideae - Bombacoideae - Sterculioideae - Helicteroideae - Byttnerioideae - Sapindales - Anacardiaceae - Burseraceae - Meliaceae - Rutaceae - Sapindaceae - Vitaceae - Caryophyllales - Polygonaceae - Droseraceae - Nepenthaceae - core Caryophyllales - Cactaceae - Amaranthaceae - Asterids - Ericales - Actinidiaceae - Ericaceae - Lecythidaceae - Sapotaceae - Ebenaceae - Theaceae - Solanales - Solanaceae - Convolvulaceae - Lamiales - Oleaceae - Fraxinus - Bignoniaceae - Pedaliaceae - Lentibulariaceae - Lamiaceae - Gentianales - Rubiaceae - Asterales - Campanulaceae - Asteraceae - Carduoideae - Cardueae - Cichorioideae - Cichorieae - Asteroideae - Asterodae - Helianthodae - Apiales - Apiaceae - Araliaceae - Aquifoliaceae - Fungi - Fungi 1 - Dikarya - Basidiomycota - Agaricomycotina - Agaricomycetes - Agaricomycetes 1 - Agaricomycetidae - Agaricales - Strophariaceae strict-sense - Psathyrellaceae - Agaricaceae - Nidulariaceae - Marasmiaceae - Physalacriaceae - Pleurotaceae - Amanitaceae - Podoserpula - Boletales - Serpulaceae - Sclerodermataceae - Boletaceae - Russulales - Hymenochaetales - Phallomycetidae - Geastrales - Gomphales - Phallales - Cantharellales - Auriculariales - Tremellomycetes - Ustilaginomycotina - Pucciniomycotina - Pucciniomycetes - Septobasidiales - Pucciniales - Mixiomycetes - Tritirachiomycetes - Entorrhizomycetes - Wallemiomycetes - Ascomycota - Pezizomycotina - Pezizomycetes - 'Leotiomyceta' - Eurotiomycetes - Geoglossaceae - Sordariomycetes - Hypocreomycetidae - Sordariomycetidae - Laboulbeniomycetes - Pleosporomycetidae - Saccharomycotina - Taphrinomycotina - Schizosaccharomycetes - Pneumocystidiomycetes - Taphrinomycetes - Glomeromycota - Zygomycota - Endogonales - Mucorales - Blastocladiomycota - Chytridiomycota - Neocallimastigomycota - Microsporidia - Animalia - Porifera - Cnidaria - Tardigrada - Annelida - Mollusca - Bivalvia - Gastropoda - Cephalopoda - Arthropoda - Arachnida - Araneae - Opiliones - Scorpiones - Heterostigmata - Crustacea - Euphausiacea - Brachyura - Isopoda - Cirripedia - Insecta - Anisoptera - Mantodea - Cicadoidea - Siphonaptera - Cucujoidea - Phengodidae - Drosophilidae - Culicidae - Lepidoptera - Apini - Formicidae - Deuterostomia - Echinodermata - Crinoidea - Asteroidea - Echinoidea - Holothuroidea - Vertebrata - Chondrichthyes - Carcharodon carcharias - Rhinocodon typus - Batoidea - Pristidae - Actinopterygii - Clupeomorpha - Xiphias gladius - Siluriformes - Carassius auratus - Tetraodontidae - Molidae - Gymnotiformes - Lophiiformes - Exocoetidae - 'mudskipper' - Hippocampus - Psudoliparis swirei - Sarcopterygii - Tetrapoda - Amphibia - Gymnophiona - Caudata - Salamandra - Cryptobranchidae - Ambystomatidae - Anura - Reptilia - Testudines - Plesiosauria - Chamaeleonidae - Serpentes - Crocodilia - Dinosauria - Triceratops - Sauropoda - Tyrannosauroidea - Aves - magpie - parrot - eagle - owl - swan - chicken - penguin - hummingbird - Synapsida - monotreme - marsupial - kangaroo - possum - wombat - rodent - mouse - beaver - rabbit - feline - canine - bear - walrus - Artiodactyla - pig - camel - deer - giraffe - horse - elephant - cetacean - armadillo - bat - monkey - gorilla - chimpanzee - homo sapien diff --git a/data_tol_old/txtTreeToJSON.py b/data_tol_old/txtTreeToJSON.py deleted file mode 100755 index 3b77622..0000000 --- a/data_tol_old/txtTreeToJSON.py +++ /dev/null @@ -1,76 +0,0 @@ -#!/usr/bin/python3 - -import sys, re - -usageInfo = f"usage: {sys.argv[0]}\n" -usageInfo += "Reads, from stdin, tab-indented lines representing trees, and outputs corresponding JSON.\n" - -if len(sys.argv) > 1: - print(usageInfo, file=sys.stderr) - sys.exit(1) - -lineNum = 0 -trees = [] #each node is a pair holding a name and an array of child nodes -nodeList = [] -while True: - #read line - line = sys.stdin.readline() - if line == "": break - line = line.rstrip() - lineNum += 1 - #create node - match = re.match(r"^\t*", line) - indent = len(match.group()) - newNode = [line[indent:], []] - #add node - if indent == len(nodeList): #sibling or new tree - if len(nodeList) == 0: - nodeList.append(newNode) - trees.append(newNode) - else: - nodeList[-1] = newNode - if len(nodeList) == 1: - trees[-1][1].append(newNode) - else: - nodeList[-2][1].append(newNode) - elif indent == len(nodeList) + 1: #direct child - if len(nodeList) == 0: - print(f"ERROR: Child without preceding root (line {lineNum})") - sys.exit(1) - nodeList.append(newNode) - nodeList[-2][1].append(newNode) - elif indent < len(nodeList): #ancestor sibling or new tree - nodeList = nodeList[:indent] - if len(nodeList) == 0: - nodeList.append(newNode) - trees.append(newNode) - else: - nodeList[-1] = newNode - if len(nodeList) == 1: - trees[-1][1].append(newNode) - else: - nodeList[-2][1].append(newNode) - else: - print(f"ERROR: Child with invalid relative indent (line {lineNum})") - sys.exit(1) -#print as JSON -if len(trees) > 1: - print("[") -def printNode(node, indent): - if len(node[1]) == 0: - print(indent + "{\"name\": \"" + node[0] + "\"}", end="") - else: - print(indent + "{\"name\": \"" + node[0] + "\", \"children\": [") - for i in range(len(node[1])): - printNode(node[1][i], indent + "\t") - if i < len(node[1])-1: - print(",", end="") - print() - print(indent + "]}", end="") -for i in range(len(trees)): - printNode(trees[i], "") - if i < len(trees)-1: - print(",", end="") - print() -if len(trees) > 1: - print("]") |