refactor: ignore missing variables for now

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Author: JoshLoecker

main/COMO.ipynb

@@ -442,7 +442,7 @@
     }
    ],
    "source": [
-    "from como.rnaseq_gen import rnaseq_gen, FilteringTechnique\n",
+    "from como.rnaseq_gen import FilteringTechnique, rnaseq_gen\n",
     "\n",
     "replicate_ratio = 0.75\n",
     "high_confidence_replicate_ratio = 1.0\n",
@@ -452,7 +452,7 @@
     "cutoff = -3\n",
     "\n",
     "for i, context in enumerate(context_names):\n",
-    "    await rnaseq_gen(  # noqa\n",
+    "    await rnaseq_gen(\n",
     "        context_name=context,\n",
     "        input_rnaseq_filepath=trna_matrix_filepath[i],\n",
     "        input_gene_info_filepath=gene_info_filepath[i],\n",
@@ -494,7 +494,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from como.rnaseq_gen import rnaseq_gen, FilteringTechnique\n",
+    "from como.rnaseq_gen import FilteringTechnique, rnaseq_gen\n",
     "\n",
     "replicate_ratio = 0.75\n",
     "high_confidence_replicate_ratio = 1.0\n",
@@ -546,7 +546,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from como.rnaseq_gen import rnaseq_gen, FilteringTechnique\n",
+    "from como.rnaseq_gen import FilteringTechnique, rnaseq_gen\n",
     "\n",
     "replicate_ratio = 0.75\n",
     "high_confidence_replicate_ratio = 1.0\n",
@@ -744,8 +744,8 @@
     "    [\n",
     "        \"python3\", \"como/merge_xomics.py\",\n",
     "        \"--merge-zfpkm-distribution\",\n",
-    "        \"--total-rnaseq-config-file\", trnaseq_config_file,\n",
-    "        \"--mrnaseq-config-file\", mrnaseq_config_file,\n",
+    "        \"--total-rnaseq-config-file\", trnaseq_config_file,  # noqa: F821\n",
+    "        \"--mrnaseq-config-file\", mrnaseq_config_file,  # noqa: F821\n",
     "        # \"--scrnaseq-config-file\", scrnaseq_config_file,  # If using single-cell data, uncomment the start of this line\n",
     "        # \"--proteomics-config-file\", proteomics_config_file,  # If using proteomics data, uncomment the start of this line\n",
     "        \"--requirement-adjust\", requirement_adjust,\n",