restructured command line tools

* documentation removed for unsupported tools * bcmembers is now part of subtypes * causalinf-pre, causalinf-post and neo are deprecated * version number increment
baliga-lab · Sep 6, 2024 · 041dbf7 · 041dbf7
1 parent 318568e
commit 041dbf7
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diff --git a/bin/miner3-bcmembers b/bin/miner3-bcmembers
diff --git a/bin/miner3-subtypes b/bin/miner3-subtypes
@@ -56,4 +56,5 @@ if __name__ == '__main__':
     with open(args.regulons) as infile:
         regulon_modules = json.load(infile)
 
+    bcmembers.bcmembers(exp_data, regulon_modules, args.outdir)
     subtypes.subtypes(exp_data, regulon_modules, args.outdir)
diff --git a/docs/conf.py b/docs/conf.py
@@ -26,7 +26,7 @@
 # The short X.Y version
 version = '3.0'
 # The full version, including alpha/beta/rc tags
-release = '1.1.9'
+release = '1.2.1'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/index.rst b/docs/index.rst
@@ -15,11 +15,7 @@ from experimental data.
 
    miner3-coexpr <miner_coexpr>
    miner3-mechinf <miner_mechinf>
-   miner3-bcmembers <miner_bcmembers>
    miner3-subtypes <miner_subtypes>
    miner3-survival <miner_survival>
-   miner3-causalinf-pre <miner_causalinf_pre>
-   miner3-neo <miner_neo>
-   miner3-causalinf-post <miner_causalinf_post>
    miner3-causalinference <miner_causalinference>
    miner3-riskpredict <miner_riskpredict>
diff --git a/docs/miner_bcmembers.rst b/docs/miner_bcmembers.rst
diff --git a/docs/miner_causalinf_post.rst b/docs/miner_causalinf_post.rst
diff --git a/docs/miner_causalinf_pre.rst b/docs/miner_causalinf_pre.rst
diff --git a/docs/miner_neo.rst b/docs/miner_neo.rst
diff --git a/docs/miner_subtypes.rst b/docs/miner_subtypes.rst
@@ -39,6 +39,12 @@ Output in detail
 
 After successful completion there will be the following files in the output directory
 
+  * ``coherentMembers.csv``
+  * ``overExpressedMembers.csv``
+  * ``underExpressedMembers.csv``
+  * ``dysregulatedMembers.csv``
+  * ``overExpressedMembers.json``
+  * ``underExpressedMembers.json``
   * ``binaryActivityMap.pdf``
   * ``regulon_activity_heatmap.pdf``
   * ``centroid_clusters_heatmap.pdf``

diff --git a/setup.py b/setup.py
@@ -20,7 +20,7 @@
                     'tqdm>=4.64.0']
 setuptools.setup(
     name="isb_miner3",
-    version="1.2.0",
+    version="1.2.1",
     author="Matt Wall",
     author_email="[email protected]",
     description="MINER analysis tools",
@@ -47,7 +47,8 @@
         "Topic :: Software Development :: Libraries :: Python Modules"
     ],
     scripts=['bin/miner3-coexpr', 'bin/miner3-mechinf',
-             'bin/miner3-bcmembers', 'bin/miner3-subtypes',
-             'bin/miner3-survival', 'bin/miner3-causalinference', 'bin/miner3-causalinf-pre',
-             'bin/miner3-causalinf-post', 'bin/miner3-neo', 'bin/miner3-riskpredict',
+             'bin/miner3-subtypes',
+             'bin/miner3-survival',
+             'bin/miner3-causalinference',
+             'bin/miner3-riskpredict',
              'bin/gene2opentargets', 'bin/drug2opentargets'])