eaf7b44ce9439f1fca4764dfba18de5131995ce4
hiram
  Wed Oct 9 12:54:21 2024 -0700
fixup apicomplexans tsetse fly and tunicate

diff --git src/hg/makeDb/doc/asmHubs/commonNames.py src/hg/makeDb/doc/asmHubs/commonNames.py
index d7d47c6..589559e 100755
--- src/hg/makeDb/doc/asmHubs/commonNames.py
+++ src/hg/makeDb/doc/asmHubs/commonNames.py
@@ -57,31 +57,31 @@
            
 
             pat = re.compile(r'.*ganism name:\s+', re.IGNORECASE)
             sciName = pat.sub('', line)
             pat = re.compile(r'\s+\(.*\)$')
             sciName = pat.sub('', sciName)
             pat = re.compile(r'[()\[\]+*]')
             sciName = pat.sub('', sciName)
             pat = re.compile(r'\?')
             sciName = pat.sub(' ', sciName)
 
             pat = r'kinetoplastids|firmicutes|proteobacteria|high G|enterobacteria|agent of'
             if re.search(pat, orgName):
               orgName = sciName
             else:
-              pat = r'bugs|crustaceans|nematodes|flatworm|ascomycete|basidiomycete|budding|microsporidian|smut|fungi|eukaryotes|flies|beetles|mosquitos|bees|moths|sponges|^mites|ticks|^comb|jellies|jellyfishes|chitons|bivalves|bony fishes|birds|eudicots|snakes|bats'
+              pat = r'apicomplexans|bugs|crustaceans|nematodes|flatworm|ascomycete|basidiomycete|budding|microsporidian|smut|fungi|eukaryotes|flies|beetles|mosquitos|bees|moths|sponges|^mites|ticks|^comb|jellies|jellyfishes|chitons|bivalves|bony fishes|birds|eudicots|snakes|bats|tunicates|tsetse fly'
               if re.search(pat, orgName):
                 order = orgName.split()[0]
                 if re.search('budding', order):
                   order = "budding yeast"
                 elif re.search('smut', order):
                   order = "smut fungi"
                 elif re.search('bony', order):
                   order = "bony fish"
                 elif re.search('ascomycete', order):
                   order = "ascomycetes"
                 elif re.search('eudicots', order):
                   order = "eudicot"
                 elif re.search('birds', order):
                   order = "bird"
                 elif re.search('snakes', order):
@@ -108,32 +108,38 @@
                   order = "bat"
                 elif re.search('moths', order):
                   order = "moth"
                 elif re.search('sponges', order):
                   order = "sponge"
                 elif re.search('flatworms', order):
                   order = "flatworm"
                 elif re.search('nematodes', order):
                   order = "nematode"
                 elif re.search('basidiomycete', order):
                   order = "basidiomycetes"
                 words = sciName.split()
                 restWords = " ".join(words[1:])
                 if re.search("eukaryotes", orgName):
                   orgName = words[0][0].upper() + "." + restWords
+                elif re.search("apicomplexans", orgName):
+                  orgName = "apicomplexans " + words[0][0].upper() + "." + restWords
                 elif re.search("flies", orgName):
                   orgName = "fly " + words[0][0].upper() + "." + restWords
+                elif re.search("tsetse", orgName):
+                  orgName = "tsetse fly " + words[0][0].upper() + "." + restWords
+                elif re.search("tunicates", orgName):
+                  orgName = "tunicate " + words[0][0].upper() + "." + restWords
                 else:
                   orgName = order + " " + words[0][0].upper() + "." + restWords
               elif re.search("viruses", orgName):
                 orgName = saveOrgName
                 pat = re.compile(r'.*ism name:\s+')
                 orgName = pat.sub('', orgName)
                 pat = re.compile(r'\s+\(.*\)$')
                 orgName = pat.sub('', orgName)
 
           elif "Date:" in line:
             words = line.split()
             pat = re.compile(r'-.*')
             yearDate = pat.sub('', words[-1])
           elif "Isolate:" in line:
             pat = re.compile(r'.*solate:\s+')