v1.0.5

Author: francois-a

Dockerfile

@@ -52,7 +52,7 @@ RUN pip3 install numpy pandas scipy
 RUN pip3 install pandas-plink ipython jupyter matplotlib pyarrow torch rpy2 gcsfs
 
 RUN cd /opt && \
-    wget https://github.com/broadinstitute/tensorqtl/archive/v1.0.4.tar.gz && \
-    tar -xf v1.0.4.tar.gz && mv tensorqtl-1.0.4 tensorqtl && \
-    rm v1.0.4.tar.gz
+    wget https://github.com/broadinstitute/tensorqtl/archive/v1.0.5.tar.gz && \
+    tar -xf v1.0.5.tar.gz && mv tensorqtl-1.0.5 tensorqtl && \
+    rm v1.0.5.tar.gz
 RUN pip3 install -e /opt/tensorqtl/

example/tensorqtl_examples.ipynb

@@ -44,15 +44,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "PyTorch 1.6.0\n",
-      "Pandas 1.1.1\n"
+      "PyTorch 1.7.1\n",
+      "Pandas 1.2.2\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Mapping files: 100%|██████████| 3/3 [00:27<00:00,  9.27s/it]\n"
+      "Mapping files: 100%|██████████| 3/3 [00:19<00:00,  6.52s/it]\n"
      ]
     }
    ],
@@ -101,11 +101,10 @@
       "  * 301 phenotypes\n",
       "  * 26 covariates\n",
       "  * 13369268 variants\n",
-      "  * checking phenotypes: 301/301\n",
       "  * Computing associations\n",
       "    Mapping chromosome chr18\n",
       "    processing phenotype 301/301\n",
-      "    time elapsed: 0.03 min\n",
+      "    time elapsed: 0.04 min\n",
       "    * writing output\n",
       "done.\n"
      ]
@@ -275,10 +274,9 @@
       "  * 26 covariates\n",
       "  * 13369268 variants\n",
       "  * using seed 123456\n",
-      "  * checking phenotypes: 301/301\n",
       "  * computing permutations\n",
       "    processing phenotype 301/301\n",
-      "  Time elapsed: 0.54 min\n",
+      "  Time elapsed: 0.34 min\n",
       "done.\n"
      ]
     }
@@ -522,7 +520,7 @@
       "  * 26 covariates\n",
       "  * 13369268 variants\n",
       "    processing batch 1337/1337\n",
-      "    elapsed time: 1.41 min\n",
+      "    elapsed time: 0.67 min\n",
       "  * 7620376 variants passed MAF >= 0.05 filtering\n",
       "done.\n"
      ]
@@ -678,7 +676,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

tensorqtl/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "1.0.4"
+__version__ = "1.0.5"
 from .tensorqtl import *