From 0123108586dbb4ddfd8aa07d01c8a53a9c6b584b Mon Sep 17 00:00:00 2001
From: dvklopfenstein <dvklopfenstein@users.noreply.github.com>
Date: Mon, 1 Apr 2019 17:27:45 -0400
Subject: [PATCH] updsates

---
 log/reactome_data_schema.txt | 37 +++++++++++++--------------
 src/bin/describe_pathway.py  | 49 ------------------------------------
 2 files changed, 18 insertions(+), 68 deletions(-)
 delete mode 100755 src/bin/describe_pathway.py

diff --git a/log/reactome_data_schema.txt b/log/reactome_data_schema.txt
index aa4c9cb..c428b9a 100644
--- a/log/reactome_data_schema.txt
+++ b/log/reactome_data_schema.txt
@@ -1,8 +1,8 @@
 TOP DATA SCHEMA: DatabaseObject
 ------------------------------------
-- DatabaseObject(dcnt=80)
--- PhysicalEntity(dcnt=13)
+- DatabaseObject(dcnt=79)
 -- AbstractModifiedResidue(dcnt=12)
+-- PhysicalEntity(dcnt=12)
 -- Event(dcnt=8)
 -- ReferenceEntity(dcnt=8)
 -- Regulation(dcnt=5)
@@ -27,21 +27,6 @@ TOP DATA SCHEMA: DatabaseObject
 DEPTH-01 DATA SCHEMA: DatabaseObject
 ------------------------------------
 
-- PhysicalEntity(dcnt=13)
--- EntitySet(dcnt=3)
---- CandidateSet(dcnt=0)
---- DefinedSet(dcnt=0)
---- OpenSet(dcnt=0)
--- Drug(dcnt=2)
---- ChemicalDrug(dcnt=0)
---- ProteinDrug(dcnt=0)
--- GenomeEncodedEntity(dcnt=1)
---- EntityWithAccessionedSequence(dcnt=0)
--- Complex(dcnt=0)
--- OtherEntity(dcnt=0)
--- Polymer(dcnt=0)
--- SimpleEntity(dcnt=0)
-
 - AbstractModifiedResidue(dcnt=12)
 -- GeneticallyModifiedResidue(dcnt=5)
 --- FragmentModification(dcnt=3)
@@ -56,6 +41,20 @@ DEPTH-01 DATA SCHEMA: DatabaseObject
 --- GroupModifiedResidue(dcnt=0)
 --- ModifiedResidue(dcnt=0)
 
+- PhysicalEntity(dcnt=12)
+-- Drug(dcnt=2)
+--- ChemicalDrug(dcnt=0)
+--- ProteinDrug(dcnt=0)
+-- EntitySet(dcnt=2)
+--- CandidateSet(dcnt=0)
+--- DefinedSet(dcnt=0)
+-- GenomeEncodedEntity(dcnt=1)
+--- EntityWithAccessionedSequence(dcnt=0)
+-- Complex(dcnt=0)
+-- OtherEntity(dcnt=0)
+-- Polymer(dcnt=0)
+-- SimpleEntity(dcnt=0)
+
 - Event(dcnt=8)
 -- ReactionLikeEvent(dcnt=5)
 --- BlackBoxEvent(dcnt=0)
@@ -63,8 +62,8 @@ DEPTH-01 DATA SCHEMA: DatabaseObject
 --- FailedReaction(dcnt=0)
 --- Polymerisation(dcnt=0)
 --- Reaction(dcnt=0)
--- Pathway(dcnt=1)
---- TopLevelPathway(dcnt=0)
+-- Pathway(dcnt=0)
+-- TopLevelPathway(dcnt=0)
 
 - ReferenceEntity(dcnt=8)
 -- ReferenceSequence(dcnt=4)
diff --git a/src/bin/describe_pathway.py b/src/bin/describe_pathway.py
deleted file mode 100755
index 2fd051c..0000000
--- a/src/bin/describe_pathway.py
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env python
-"""Describe the Pathway(s) requested by user."""
-
-__copyright__ = "Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved."
-__author__ = "DV Klopfenstein"
-
-import os
-import sys
-from goatools.obo_parser import GODag
-# from goatools.base import get_godag
-# from goatools.base import dnld_gaf
-from goatools.associations import read_gaf
-from goatools.semantic import TermCounts
-from goatools.gosubdag.gosubdag import GoSubDag
-from reactomepy.code.wrpy.utils import REPO
-from reactomepy.code.describe_pathway import DescribePathway
-
-
-def main(obo='go-basic.obo', gaf='goa_human.gaf'):
-    """Describe the Pathway(s) requested by user."""
-    gosubdag = _get_gosubdag(obo, gaf)
-    obj = DescribePathway('hsa', gosubdag)
-    pmids = obj.get_pwys_w_all()
-    # return
-    print('{N} Pathways of {M} have all types of data'.format(N=len(pmids), M=len(obj.pw2nt)))
-    obj.prt_pw('R-HSA-202040')
-    obj.prt_pw('R-HSA-168898')   # Multiple Species
-    obj.prt_pw('R-HSA-5678420')  # Multiple diseases
-    obj.prt_pw('R-HSA-15869')    # Biological Pathways
-    obj.prt_pw('R-HSA-71288')    # Cellular Components
-    # print(gosubdag.prt_attr)
-    # print(gosubdag.prt_attr['fmt'])
-
-def _get_gosubdag(obo, gaf):
-    """Return a gosubdag object with human annotations."""
-    # Load GO DAG with optional 'definition' field values
-    godag = GODag(os.path.join(REPO, obo), ['defn'])
-    # Annotations
-    #   % wget http://geneontology.org/gene-associations/goa_human.gaf.gz
-    #   % gunzip goa_human.gaf.gz
-    gene2gos = read_gaf(gaf)
-    tcntobj = TermCounts(godag, gene2gos)
-    return GoSubDag(None, godag, tcntobj=tcntobj, prt=sys.stdout)
-
-
-if __name__ == '__main__':
-    main()
-
-# Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved.