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@hackerb9 hackerb9/lookup.py
Last active Nov 4, 2019

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Simplest example of parsing text files of ITIS taxonomy
#!/usr/bin/python3
# globals
name={}
hierarchy={}
vernacular={}
synonyms={}
def loaddb():
"Load up databases into dictionaries: name, hierarchy, vernacular"
global name, hierarchy, vernacular, synonyms
# Slurp up conversion from taxonomic serial number x to longname y
f=open("longnames", "rb")
for line in f:
line=line.decode('latin-1')
(x,y) = line.split('|')
name[x]=y.rstrip()
f.close()
# Load in hierarchy, mapping taxonomic serial number n to hierarchy h
f=open("hierarchy", "rb")
for line in f:
line=line.decode('latin-1')
(h,n,*dummy) = line.split('|')
hierarchy[n]=h.rstrip()
f.close()
# Read in the vernacular database (mapping 'European frog' to '173444')
f=open("vernaculars", "rb")
for line in f:
line=line.decode('latin-1')
(n,v,*dummy) = line.split('|')
v=v.lower()
if v not in vernacular:
vernacular[v]=[]
vernacular[v].append(n)
f.close()
# Read in the synonyms database (mapping obsolete TSN to current TSN)
f=open("synonym_links", "rb")
for line in f:
line=line.decode('latin-1')
(n,s,dummy) = line.split('|')
synonyms[n]=s
f.close()
def printhierarchy(v):
# Look up by vernacular and print hierarchy
try:
vlist=vernacular[v.lower()]
# Print out the hierarchy
for n in vlist:
if n in hierarchy:
h=hierarchy[n]
elif n in synonyms:
h=hierarchy[synonyms[n]]
else:
return False
print( v + ':' )
for level in h.split('-'):
print ( ' → ' + name[level] )
except KeyError:
print( "‘"+v+"’ not found" )
# Main
loaddb()
from sys import argv
arg=' '.join( [ str(x) for x in argv[1:] ] )
printhierarchy(arg)
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