Return gamma delta notebook (#250)

* Create gamma_delta.ipynb

* black updated...

* Update gamma_delta.ipynb

typo

dandelion/plotting/_plotting.py

@@ -138,11 +138,7 @@ def clone_rarefaction(
             n = np.append(n, tot[i])
         rarecurve[res_.index[i]] = [
             rarefun(
-                np.array(
-                    res_.iloc[
-                        i,
-                    ]
-                ),
+                np.array(res_.iloc[i,]),
                 z,
             )
             for z in n

dandelion/preprocessing/_preprocessing.py

@@ -2005,12 +2005,8 @@ def _create_germlines_object(
                 # Define Receptor iterator
                 receptor_iter = (
                     (
-                        data.data.loc[
-                            x,
-                        ].sequence_id,
-                        data.data.loc[
-                            x,
-                        ],
+                        data.data.loc[x,].sequence_id,
+                        data.data.loc[x,],
                     )
                     for x in data.data.index
                 )
@@ -2042,12 +2038,8 @@ def _create_germlines_object(
             # Define Receptor iterator
             receptor_iter = (
                 (
-                    data.loc[
-                        x,
-                    ].sequence_id,
-                    data.loc[
-                        x,
-                    ],
+                    data.loc[x,].sequence_id,
+                    data.loc[x,],
                 )
                 for x in data.index
             )
@@ -2741,7 +2733,6 @@ def quantify_mutations(
     if region_definition is None:
         reg_d = NULL
     else:
-
         reg_d = base.get(region_definition)
 
     if mutation_definition is None:
@@ -3392,7 +3383,6 @@ def __init__(
                 h_locus_p = list(data1["locus"])
                 if len(h_p) > 1:
                     if "sequence_alignment" in data1:
-
                         (
                             data1,
                             h_p,
@@ -3423,7 +3413,6 @@ def __init__(
                         sum_umi = sum(h_umi_p)
                         if "IGHD" in h_ccall_p:
                             if all(x in ["IGHM", "IGHD"] for x in h_ccall_p):
-
                                 h_ccall_p_igm_count = dict(
                                     data1[data1["c_call"] == "IGHM"][
                                         "duplicate_count"

dandelion/tools/_diversity.py

@@ -104,11 +104,7 @@ def clone_rarefaction(
             n = np.append(n, tot[i])
         rarecurve[res_.index[i]] = [
             rarefun(
-                np.array(
-                    res_.iloc[
-                        i,
-                    ]
-                ),
+                np.array(res_.iloc[i,]),
                 z,
             )
             for z in n

dandelion/tools/_network.py

@@ -1125,7 +1125,6 @@ def nx2gt(nxG):
     # Add the node properties first
     nprops = set()  # cache keys to only add properties once
     for node, data in list(nxG.nodes(data=True)):
-
         # Go through all the properties if not seen and add them.
         for key, val in data.items():
             if key in nprops:
@@ -1148,7 +1147,6 @@ def nx2gt(nxG):
     # Add the edge properties second
     eprops = set()  # cache keys to only add properties once
     for src, dst, data in list(nxG.edges(data=True)):
-
         # Go through all the edge properties if not seen and add them.
         for key, val in data.items():
             if key in eprops:
@@ -1167,7 +1165,6 @@ def nx2gt(nxG):
     # Add the nodes
     vertices = {}  # vertex mapping for tracking edges later
     for node, data in list(nxG.nodes(data=True)):
-
         # Create the vertex and annotate for our edges later
         v = gtG.add_vertex()
         vertices[node] = v
@@ -1179,7 +1176,6 @@ def nx2gt(nxG):
 
     # Add the edges
     for src, dst, data in list(nxG.edges(data=True)):
-
         # Look up the vertex structs from our vertices mapping and add edge.
         e = gtG.add_edge(vertices[src], vertices[dst])
 

dandelion/utilities/_core.py

@@ -2351,7 +2351,6 @@ def initialize_metadata(
     vdj_gene_calls = ["v_call", "d_call", "j_call"]
     if collapse_alleles:
         for x in vdj_gene_calls:
-
             if x in vdj_data.data:
                 for c in tmp_metadata:
                     if x in c:

docs/notebooks/gamma_delta.ipynb

@@ -0,0 +1,54 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Dandelion for TCR gamma/delta reannotation\n",
+    "\n",
+    "![dandelion_logo](img/dandelion_logo_illustration.png)\n",
+    "\n",
+    "In Cell Ranger 3.1.0, the VDJ algorithm was changed to favour TCR alpha/beta annotation. Since then, calling gamma/delta chains has become challenging, and 10X support recommends using Cell Ranger 3.0.2 when working with gamma/delta-rich libraries. \n",
+    "\n",
+    "However, the contigs themselves are still accurately reconstructed, just not annotated correctly. It may be desirable to use a newer Cell Ranger version for access to some previously unavailable run options, like specifying custom enrichment primers. In those cases, the contigs can be reannotated via `dandelion` to yield functional output.\n",
+    "\n",
+    "Just follow [standard protocol](https://sc-dandelion.readthedocs.io/en/latest/notebooks/Q1-singularity-preprocessing.html) for preparing and running the preprocessing. The parameterisation recommendation is applicable here as well:\n",
+    "\n",
+    "```bash\n",
+    "singularity run -B $PWD /path/to/sc-dandelion_latest.sif dandelion-preprocess \\\n",
+    "     --chain TR \\\n",
+    "     --file_prefix all \\\n",
+    "     --filter_to_high_confidence\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}