fix os and glob

gaow · Jul 1, 2019 · 69d4049 · 69d4049
1 parent fb1a83c
commit 69d4049
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Showing 3 changed files with 10 additions and 4 deletions.
diff --git a/workflow/finemapping_results_wrangler.ipynb b/workflow/finemapping_results_wrangler.ipynb
@@ -370,6 +370,7 @@
     "parameter: columns = [2,4]\n",
     "# chromosome identifiers\n",
     "parameter: chroms = [x+1 for x in range(22)]\n",
+    "import glob\n",
     "skip_if(len(glob.glob(f\"{id_map_prefix:a}.*.{id_map_suffix}\")) == 0, msg = 'Variant ID are not updated because no valid file is found using --id-map-prefix and --id-map-suffix')\n",
     "output: f'{_input:n}.id_updated.gz'\n",
     "R: expand = \"${ }\", stdout = f'{_output:n}.log'\n",
@@ -427,6 +428,7 @@
     "parameter: columns = [2,4,5,6]\n",
     "# chromosome identifiers\n",
     "parameter: chroms = [x+1 for x in range(22)]\n",
+    "import glob\n",
     "skip_if(len(glob.glob(f\"{coordinate_map_prefix:a}.*.{coordinate_map_suffix}\")) == 0, msg = 'Genomic coordinates are not updated because no valid file is found using --coordinate-map-prefix and --coordinate-map-suffix')\n",
     "output: f'{_input:n}.{coordinate_version_id}.gz'.replace('.id_updated.', '.')\n",
     "R: expand = \"${ }\", stdout = f'{_output:n}.log'\n",
@@ -506,7 +508,7 @@
      ""
     ]
    ],
-   "version": "0.18.3"
+   "version": "0.19.4"
   }
  },
  "nbformat": 4,

diff --git a/workflow/summary_statistics_finemapping.ipynb b/workflow/summary_statistics_finemapping.ipynb
@@ -280,6 +280,7 @@
     "# Whether or not to keep fit from each iteration,\n",
     "# for debug purpose.\n",
     "parameter: track_fit = False\n",
+    "import os\n",
     "#\n",
     "suffix = f'SuSiE_B.L_{L}.prior_{fmtP(susie_pve)}.res_var_{str(susie_est_residual).lower()}'\n",
     "var_y_str = f'var_y = {var_y},' if var_y > 0 else ''\n",
@@ -345,6 +346,7 @@
     "# Whether or not to keep fit from each iteration,\n",
     "# for debug purpose.\n",
     "parameter: track_fit = False\n",
+    "import os\n",
     "#\n",
     "suffix = f'SuSiE_Z.L_{L}'\n",
     "#\n",
@@ -405,6 +407,7 @@
     "fail_if(n<=2, msg = 'Please specif valid sample size --n')\n",
     "# Extra arguments to pass to DAP\n",
     "parameter: args = ''\n",
+    "import os\n",
     "suffix = f'DAP{\".\"+fmtP(args) if len(args) else \"\"}'\n",
     "#\n",
     "depends: executable('dap-g'), Py_Module('pandas'), Py_Module('numpy')\n",
@@ -1549,7 +1552,7 @@
     "height": 0,
     "style": "side"
    },
-   "version": "0.18.3"
+   "version": "0.19.4"
   }
  },
  "nbformat": 4,

diff --git a/workflow/summary_statistics_wrangler.ipynb b/workflow/summary_statistics_wrangler.ipynb
@@ -77,7 +77,7 @@
     "  ```\n",
     "  where each line is white-space separated with the first the chromosome number and second the file name.\n",
     "  \n",
-    "  **For UChicago midway users**: reference genotype data for 1000 Genomes EUR samples are extracted using workflow `prepare_1KG_reference` below. The output can be found under `/project/mstephens/SuSIE_gtex_CPP/1KG_EUR`. The manifest file `1KG_EUR.manifest` was prepared by:\n",
+    "  **For UChicago midway users**: reference genotype data for 1000 Genomes EUR samples are extracted using workflow `prepare_1KG_reference` below. The output can be found under `/project2/xinhe/mqiao/SuSiE_GWAS/1KG_EUR/`. The manifest file `1KG_EUR.manifest` was prepared by:\n",
     "  ```\n",
     "  for i in {1..22} X; do echo $i ALL.chr$i.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.EUR.vcf.gz; done > 1KG_EUR.manifest\n",
     "  ```"
@@ -414,6 +414,7 @@
     "parameter: adjust_panel_position = 1\n",
     "# Either empty, or `chr`\n",
     "parameter: panel_chrom_prefix = ''\n",
+    "import os\n",
     "\n",
     "fail_if(len(columns) not in (5,6), msg = 'Input column ID has to be of length 5 or 6.')\n",
     "\n",
@@ -1209,7 +1210,7 @@
     "height": 0,
     "style": "side"
    },
-   "version": "0.18.4"
+   "version": "0.19.4"
   }
  },
  "nbformat": 4,