Fixes biocommons#614: update doc to match relocated AssemblyMapper

ecalifornica · Jun 1, 2021 · 4c7b45f · 4c7b45f
1 parent 8b3e0f7
commit 4c7b45f
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Showing 7 changed files with 9 additions and 9 deletions.
diff --git a/docs/examples/manuscript-example.rst b/docs/examples/manuscript-example.rst
@@ -50,7 +50,7 @@ Project transcript variant NM_182763.2:c.688+403C>T to GRCh37 primary assembly u
 .. code:: 
 
     import hgvs.variantmapper
-    vm = hgvs.variantmapper.AssemblyMapper(
+    vm = hgvs.assemblymapper.AssemblyMapper(
         hdp, assembly_name='GRCh37', alt_aln_method='splign')
     var_g = vm.c_to_g(var_c1)
     var_g

diff --git a/docs/examples/using-hgvs.rst b/docs/examples/using-hgvs.rst
@@ -210,8 +210,8 @@ assembly.
 
     import hgvs.variantmapper
     #vm = variantmapper = hgvs.variantmapper.VariantMapper(hdp)
-    am37 = easyvariantmapper = hgvs.variantmapper.AssemblyMapper(hdp, assembly_name='GRCh37')
-    am38 = easyvariantmapper = hgvs.variantmapper.AssemblyMapper(hdp, assembly_name='GRCh38')
+    am37 = easyvariantmapper = hgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37')
+    am38 = easyvariantmapper = hgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh38')
 
 c_to_g
 ~~~~~~

diff --git a/examples/hgvs-poster.ipynb b/examples/hgvs-poster.ipynb
@@ -61,7 +61,7 @@
     "hdp = hgvs.dataproviders.uta.connect()\n",
     "\n",
     "import hgvs.variantmapper\n",
-    "am = hgvs.variantmapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign')"
+    "am = hgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign')"
    ]
   },
   {

diff --git a/examples/hgvs-rapid-fire.ipynb b/examples/hgvs-rapid-fire.ipynb
@@ -23,7 +23,7 @@
    "source": [
     "hp = hgvs.parser.Parser()\n",
     "hdp = hgvs.dataproviders.uta.connect()\n",
-    "am = hgvs.variantmapper.AssemblyMapper(hdp,\n",
+    "am = hgvs.assemblymapper.AssemblyMapper(hdp,\n",
     "                                           assembly_name='GRCh37',\n",
     "                                           alt_aln_method='splign')"
    ]

diff --git a/examples/manuscript-example.ipynb b/examples/manuscript-example.ipynb
@@ -103,7 +103,7 @@
      "collapsed": false,
      "input": [
       "import hgvs.variantmapper\n",
-      "vm = hgvs.variantmapper.AssemblyMapper(\n",
+      "vm = hgvs.assemblymapper.AssemblyMapper(\n",
       "    hdp, assembly_name='GRCh37', alt_aln_method='splign')\n",
       "var_g = vm.c_to_g(var_c1)\n",
       "var_g"

diff --git a/examples/using-hgvs.ipynb b/examples/using-hgvs.ipynb
@@ -368,8 +368,8 @@
    "source": [
     "import hgvs.variantmapper\n",
     "#vm = variantmapper = hgvs.variantmapper.VariantMapper(hdp)\n",
-    "am37 = easyvariantmapper = hgvs.variantmapper.AssemblyMapper(hdp, assembly_name='GRCh37')\n",
-    "am38 = easyvariantmapper = hgvs.variantmapper.AssemblyMapper(hdp, assembly_name='GRCh38')"
+    "am37 = easyvariantmapper = hgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37')\n",
+    "am38 = easyvariantmapper = hgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh38')"
    ]
   },
   {

diff --git a/tests/bin/build-ref-repl b/tests/bin/build-ref-repl
@@ -17,7 +17,7 @@ logging.basicConfig(level=logging.DEBUG)
 hdp = hgvs.dataproviders.uta.connect()
 hp = hgvsparser = hgvs.parser.Parser()
 vm = variantmapper = hgvs.variantmapper.VariantMapper(hdp)
-am = easyvariantmapper = hgvs.variantmapper.AssemblyMapper(
+am = easyvariantmapper = hgvs.assemblymapper.AssemblyMapper(
     hdp, assembly_name='GRCh37', alt_aln_method='splign')