Models: assembly names for 7 worms added

cpockrandt · Mar 10, 2021 · 229e110 · 229e110
1 parent a3ae1cf
commit 229e110
Showing 1 changed file with 7 additions and 48 deletions.
diff --git a/src/models.hpp b/src/models.hpp
@@ -1466,47 +1466,6 @@ std::string get_list_of_models()
 
 // TODO: make this a vector of vectors
 std::unordered_map<std::string, std::vector<std::string> > sequence_name_mapping = {
-//    { "marmoset",					{ "caljac" } },
-//    { "chinese_tree_shrew",			{ "tupchi" } },
-//    { "squirrel",					{ "spetri" } },
-//    { "lesser_egyptian_jerboa",		{ "jacjac" } },
-//    { "chinese_hamster",			{ "crigri" } },
-//    { "golden_hamster",				{ "mesaur" } },
-//    { "naked_mole_rat",				{ "hetgla" } },
-//    { "chinchilla",					{ "chilan" } },
-//    { "brush_tailed_rat",			{ "octdeg" } },
-//    { "pika",						{ "ochpri" } },
-//    { "pig",						{ "susscr" } },
-//    { "alpaca",						{ "vicpac" } },
-//    { "wild_bactrian_camel",		{ "camfer" } },
-//    { "killer_whale",				{ "orcorc" } },
-//    { "tibetan_antelope",			{ "panhod" } },
-//    { "sheep",						{ "oviari" } },
-//    { "domestic_goat",				{ "caphir" } },
-//    { "horse",						{ "equcab" } },
-//    { "white_rhinoceros",			{ "cersim" } },
-//    { "ferret",						{ "musfur" } },
-//    { "pacific_walrus",				{ "odorosdiv" } },
-//    { "black_flying_fox",			{ "pteale" } },
-//    { "davids_myotis",				{ "myodav" } },
-//    { "microbat",					{ "myoluc" } },
-//    { "big_brown_bat",				{ "eptfus" } },
-//    { "hedgehog",					{ "erieur" } },
-//    { "shrew",						{ "sorara" } },
-//    { "star_nosed_mole",			{ "concri" } },
-//    { "elephant",					{ "loxafr" } },
-//    { "cape_elephant_shrew",		{ "eleedw" } },
-//    { "manatee",					{ "triman" } },
-//    { "cape_golden_mole",			{ "chrasi" } },
-//    { "tenrec",						{ "echtel" } },
-//    { "aardvark",					{ "oryafe" } },
-//    { "armadillo",					{ "dasnov" } },
-//    { "c_brenneri",					{ "caepb" } },
-//    { "c_remanei",					{ "caerem" } },
-//    { "c_briggsae",					{ "cb" } },
-//    { "c_japonica",					{ "caejap" } },
-//    { "c_tropicalis",               { "caesp" } },
-//    { "c_angaria",					{ "caeang" } ,
     // This is a full list of all species from the included phylogenetic trees above
     // NOTE: this has to be all lower case
     { "aalbs1",                     { } },
@@ -1574,14 +1533,14 @@ std::unordered_map<std::string, std::vector<std::string> > sequence_name_mapping
     { "crab_eating_macaque",        { "macfas5" } },
     { "crested_ibis",               { "nipnip1" } },
     { "cuckoo_roller",              { "lepdis1" } },
-    { "c_angaria",                  { } },
-    { "c_brenneri",                 { } },
-    { "c_briggsae",                 { } },
+    { "c_angaria",                  { "caeang2" } },
+    { "c_brenneri",                 { "caepb3" } },
+    { "c_briggsae",                 { "cb4" } },
     { "c_elegans",                  { "ce11" } },
-    { "c_japonica",                 { } },
-    { "c_remanei",                  { } },
-    { "c_sp__5_ju800",              { } },
-    { "c_tropicalis",               { } },
+    { "c_japonica",                 { "caejap4" } },
+    { "c_remanei",                  { "caerem4" } },
+    { "c_sp__5_ju800",              { "caesp51" } },
+    { "c_tropicalis",               { "caesp111" } },
     { "dalb",                       { "droalb1" } },
     { "dalmatian_pelican",          { "pelcri1" } },
     { "dana",                       { "droana3" } },