update to dms_variants 1.5.0 (#25)

* update to `dms_variants` 1.5.0

* format with newest version of `black`

* update `dms_variants` in `count_barcodes.yml` env

CHANGELOG.md

@@ -1,5 +1,8 @@
 # CHANGELOG
 
+### version 2.0.1
+- Update to `dms_variants` 1.5.0 (addresses [this issue](https://github.com/jbloomlab/seqneut-pipeline/issues/24))
+
 ## version 2.0.0
 Full re-write that changes how configuration is specified to automatically do the QC, and uses a newer version of `neutcurve` that fits better. Completely backward-incompatible with version 1.*.
 

environment.yml

@@ -20,5 +20,5 @@ dependencies:
   - snakemake=8.0.1
   - ruff
   - pip:
-    - dms_variants==1.4.3
+    - dms_variants==1.5.0
     - neutcurve==1.1.2

envs/count_barcodes.yml

@@ -10,4 +10,4 @@ dependencies:
   - pip
   - python=3.11
   - pip:
-    - dms_variants==1.4.3
+    - dms_variants==1.5.0

funcs.smk

@@ -4,7 +4,6 @@ Designed to be included in another ``Snakefile`` that specifies the config.
 
 """
 
-
 import copy
 import functools
 import os

notebooks/process_plate.py.ipynb

@@ -593,9 +593,11 @@
     "            height=alt.Step(10),\n",
     "            width=300,\n",
     "            title=alt.TitleParams(\n",
-    "                f\"{plate} all samples, neut-standard barcodes\"\n",
-    "                if is_neut_standard\n",
-    "                else f\"{plate} no-serum samples, all barcodes\",\n",
+    "                (\n",
+    "                    f\"{plate} all samples, neut-standard barcodes\"\n",
+    "                    if is_neut_standard\n",
+    "                    else f\"{plate} no-serum samples, all barcodes\"\n",
+    "                ),\n",
     "                subtitle=\"x-axis is zoomable (use mouse scroll/pan)\",\n",
     "            ),\n",
     "        )\n",
@@ -678,9 +680,11 @@
     "            legend=alt.Legend(titleLimit=500),\n",
     "        ),\n",
     "        tooltip=[\n",
-    "            alt.Tooltip(c, format=\".3g\")\n",
-    "            if neut_standard_counts[c].dtype == float\n",
-    "            else c\n",
+    "            (\n",
+    "                alt.Tooltip(c, format=\".3g\")\n",
+    "                if neut_standard_counts[c].dtype == float\n",
+    "                else c\n",
+    "            )\n",
     "            for c in neut_standard_counts.columns\n",
     "        ],\n",
     "    )\n",
@@ -856,9 +860,11 @@
     "        ),\n",
     "        color=alt.condition(strain_selection, alt.value(\"orange\"), alt.value(\"gray\")),\n",
     "        tooltip=[\n",
-    "            alt.Tooltip(c, format=\".3g\")\n",
-    "            if median_no_serum_ratio[c].dtype == float\n",
-    "            else c\n",
+    "            (\n",
+    "                alt.Tooltip(c, format=\".3g\")\n",
+    "                if median_no_serum_ratio[c].dtype == float\n",
+    "                else c\n",
+    "            )\n",
     "            for c in median_no_serum_ratio.columns\n",
     "        ],\n",
     "    )\n",
@@ -1013,9 +1019,11 @@
     "        strokeWidth=alt.condition(barcode_selection, alt.value(3), alt.value(1)),\n",
     "        opacity=alt.condition(barcode_selection, alt.value(1), alt.value(0.25)),\n",
     "        tooltip=[\n",
-    "            alt.Tooltip(c, format=\".3g\")\n",
-    "            if frac_infectivity_chart_df[c].dtype == float\n",
-    "            else c\n",
+    "            (\n",
+    "                alt.Tooltip(c, format=\".3g\")\n",
+    "                if frac_infectivity_chart_df[c].dtype == float\n",
+    "                else c\n",
+    "            )\n",
     "            for c in frac_infectivity_chart_df.columns\n",
     "        ],\n",
     "    )\n",

scripts/build_docs.py

@@ -1,6 +1,5 @@
 """Implements ``snakemake`` rule to translate gene sequence."""
 
-
 import os
 import shutil
 import sys

scripts/count_barcodes.py

@@ -1,6 +1,5 @@
 """Count barcodes from FASTQ barcodes."""
 
-
 import sys
 
 import dms_variants.illuminabarcodeparser

scripts/qc_serum_titers.py

@@ -1,6 +1,5 @@
 """Process QC for serum titers."""
 
-
 import sys
 
 

scripts/sera_by_plate.py

@@ -1,6 +1,5 @@
 """Get list of sera and plates for each."""
 
-
 import sys
 
 import pandas as pd

seqneut-pipeline.smk

@@ -4,7 +4,6 @@ Designed to be included in another ``Snakefile`` that specifies the config.
 
 """
 
-
 import pandas as pd
 
 

test_example/Snakefile

@@ -1,6 +1,5 @@
 """Top-level ``snakemake`` file that runs analysis."""
 
-
 import os
 
 

test_example/test_titers_as_expected.py

@@ -1,6 +1,5 @@
 """Test script to test titers as expected."""
 
-
 import numpy
 
 import pandas as pd