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finish up separation and Corymorpha changes

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jar398 committed Feb 26, 2017
1 parent 474cf24 commit fc5cb5c2749e9e986749281a3284d2c1df42b58d
Showing with 17 additions and 11 deletions.
  1. +2 −2 Makefile
  2. +9 −4 adjustments.py
  3. +2 −3 assemble_ott.py
  4. +2 −2 doc/method/data-package/Makefile
  5. +2 −0 inclusions.csv
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@@ -13,7 +13,7 @@
JAVAFLAGS=-Xmx14G
# Modify as appropriate
-WHICH=3.0draft5
+WHICH=3.0draft6
PREV_WHICH=2.10
# ----- Taxonomy source locations -----
@@ -111,7 +111,7 @@ tax/ott/log.tsv: $(CLASS) make-ott.py assemble_ott.py adjustments.py amendments.
bin/jython \
inclusions.csv \
feed/amendments/amendments-1/next_ott_id.json \
- tax/skel/taxonomy.tsv \
+ tax/separation/taxonomy.tsv \
feed/ott_id_list/by_qid.csv
@date
@rm -f *py.class
View
@@ -16,7 +16,8 @@ def deal_with_polysemies(ott):
# ncbi 10197 | 6072 | Ctenophora | phylum | = comb jellies OTT 641212
# ncbi 516519 | 702682 | Ctenophora | genus | = cranefly OTT 1043126
- # The comb jellies are already in the taxonomy at this point (from skeleton).
+ # The comb jellies are already in the taxonomy at this point (from
+ # separation taxonomy).
# Add the diatom to OTT so that SILVA has something to map its diatom to
# that's not the comb jellies.
@@ -28,7 +29,7 @@ def deal_with_polysemies(ott):
# Diatom. Contains e.g. Ctenophora pulchella.
establish('Ctenophora', ott, ancestor='Bacillariophyta', ott_id='103964')
- # The comb jelly should already be in skeleton, but include the code for symmetry.
+ # The comb jelly should already be in separation, but include the code for symmetry.
# Contains e.g. Leucothea multicornis
establish('Ctenophora', ott, parent='Metazoa', ott_id='641212')
@@ -72,6 +73,10 @@ def deal_with_polysemies(ott):
# not sure why this is needed.
establish('Stereopsidaceae', ott, division='Fungi', source='gbif:7717211')
+ # 3.0draft5 problem
+ establish('Corymorpha', ott, division='Cnidaria', source='ncbi:264057', ott_id='183501')
+ establish('Corymorpha', ott, division='Nematoda', source='ncbi:364543', ott_id='860265')
+
def load_silva():
silva = Taxonomy.getTaxonomy('tax/silva/', 'silva')
@@ -199,7 +204,7 @@ def fix_name(bad, good):
# JAR 2014-05-13 scrutinizing pin() and BarrierNodes. Wikipedia
# confirms this synonymy. Dail L. prefers -phyta to -phyceae
# but says -phytina would be more correct per code.
- # Skeleton taxonomy has -phyta (on Dail's advice).
+ # Separation taxonomy has -phyta (on Dail's advice).
silva.taxon('Rhodophyceae').synonym('Rhodophyta') # moot now?
silva.taxon('Florideophycidae', 'Rhodophyceae').synonym('Florideophyceae')
@@ -651,7 +656,7 @@ def patch_ncbi(ncbi):
if ncbi.maybeTaxon(toplevel) != None:
ncbi.taxon(toplevel).prune(this_source)
- # - Canonicalize division names (cf. skeleton) -
+ # - Canonicalize division names (cf. separation) -
# JAR 2014-05-13 scrutinizing pin() and BarrierNodes. Wikipedia
# confirms these synonymies.
ncbi.taxon('Glaucocystophyceae').rename('Glaucophyta')
View
@@ -34,8 +34,7 @@ def create_ott(version):
for name in names_of_interest:
ott.eventLogger.namesOfInterest.add(name)
- # idspace string 'skel' is magical, see Taxon.addSource
- ott.setSkeleton(Taxonomy.getTaxonomy('tax/skel/', 'skel'))
+ ott.setSkeleton(Taxonomy.getTaxonomy('tax/separation/', 'separation'))
# These are particularly hard cases; create alignment targets up front
adjustments.deal_with_polysemies(ott)
@@ -87,7 +86,7 @@ def merge_sources(ott):
# higher priority to Worms for Malacostraca, Cnidaria so we split out
# those clades from worms and absorb them before NCBI
worms = adjustments.load_worms()
- # Malacostraca instead of Decapoda because M. is in the skeleton
+ # Malacostraca instead of Decapoda because M. is in the separation taxonomy
(malacostraca, worms_sans_malacostraca) = split_taxonomy(worms, 'Malacostraca')
align_and_merge(ott.alignment(malacostraca))
(cnidaria, low_priority_worms) = split_taxonomy(worms_sans_malacostraca, 'Cnidaria')
@@ -14,8 +14,8 @@ ott3.0.tgz: $(REF)/tarballs/ott3.0draft3.tgz
alt-ott3.0.tgz:
wget http://files.opentreeoflife.org/ott/ott3.0/ott3.0draft3.tgz
-separation.tgz: $(REF)/tax/skel/taxonomy.tsv
- tar czf $@ -C $(REF) tax/skel
+separation.tgz: $(REF)/tax/separation/taxonomy.tsv
+ tar czf $@ -C $(REF) tax/separation
silva.tgz: $(REF)/tax/silva/taxonomy.tsv
tar czf $@ -C $(REF) tax/silva
View
@@ -108,3 +108,5 @@ Equisetidae,Equisetopsida,5662213,"issue 281"
Acropora,Cnidaria,712401,"issue reftax#298"
Acropora,Bryozoa,4149092,"issue reftax#298 (syn of Porina)"
Dermocystidium salmonis,Ichthyosporea,5653696,"issue reftax #301"
+Corymorpha,Cnidaria,183501,"fallout from setting Cnidarian priority"
+Corymorpha,Nematoda,860265,"fallout from setting Cnidarian priority"

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