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cumc · Aug 11, 2023 · 564c84a · 564c84a
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diff --git a/_sources/code/data_preprocessing/genotype/VCF_QC.ipynb b/_sources/code/data_preprocessing/genotype/VCF_QC.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "scientific-inspiration",
+   "id": "caroline-lawyer",
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "northern-primary",
+   "id": "changing-essex",
    "metadata": {
     "kernel": "SoS"
    },
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "competitive-enemy",
+   "id": "interstate-invalid",
    "metadata": {
     "kernel": "SoS"
    },
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dress-influence",
+   "id": "announced-attempt",
    "metadata": {
     "kernel": "SoS"
    },
@@ -69,7 +69,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "banner-portrait",
+   "id": "closing-cleaners",
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -94,7 +94,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "patient-catering",
+   "id": "facial-pregnancy",
    "metadata": {
     "kernel": "SoS"
    },
@@ -112,7 +112,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "inclusive-reconstruction",
+   "id": "behavioral-sequence",
    "metadata": {
     "kernel": "SoS"
    },
@@ -134,7 +134,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "wicked-teens",
+   "id": "ruled-youth",
    "metadata": {
     "kernel": "SoS"
    },
@@ -177,7 +177,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ranging-kansas",
+   "id": "psychological-understanding",
    "metadata": {
     "kernel": "SoS"
    },
@@ -192,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
-   "id": "commercial-wagon",
+   "id": "extended-bachelor",
    "metadata": {
     "kernel": "SoS"
    },
@@ -211,7 +211,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "otherwise-gnome",
+   "id": "lightweight-swedish",
    "metadata": {
     "kernel": "SoS"
    },
@@ -222,7 +222,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "tribal-product",
+   "id": "royal-prompt",
    "metadata": {
     "kernel": "SoS"
    },
@@ -241,7 +241,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "wrapped-indie",
+   "id": "passing-moral",
    "metadata": {
     "kernel": "SoS"
    },
@@ -252,7 +252,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "thorough-microwave",
+   "id": "elegant-exclusion",
    "metadata": {
     "kernel": "SoS"
    },
@@ -264,7 +264,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "approximate-patient",
+   "id": "japanese-buddy",
    "metadata": {
     "kernel": "SoS"
    },
@@ -275,7 +275,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "coupled-pipeline",
+   "id": "governmental-welcome",
    "metadata": {
     "kernel": "Bash",
     "tags": []
@@ -362,6 +362,12 @@
       "  qc_3:\n",
       "    Workflow Options:\n",
       "      --[no-]remove-duplicates (default to False)\n",
+      "      --remove-samples . (as path)\n",
+      "                        The path to the file that contains the list of samples\n",
+      "                        to remove (format FID, IID)\n",
+      "      --keep-samples . (as path)\n",
+      "                        The path to the file that contains the list of samples\n",
+      "                        to keep (format FID, IID)\n",
       "  qc_4:\n"
      ]
     }
@@ -372,7 +378,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "square-smoke",
+   "id": "liable-blocking",
    "metadata": {
     "kernel": "Bash"
    },
@@ -383,7 +389,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "thrown-wheat",
+   "id": "chubby-fishing",
    "metadata": {
     "kernel": "SoS"
    },
@@ -463,7 +469,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "paperback-requirement",
+   "id": "empirical-gasoline",
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -479,7 +485,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "brown-national",
+   "id": "lined-hungarian",
    "metadata": {
     "kernel": "SoS"
    },
@@ -501,7 +507,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "scenic-chart",
+   "id": "terminal-cleaners",
    "metadata": {
     "kernel": "SoS"
    },
@@ -532,7 +538,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "increased-complaint",
+   "id": "funky-light",
    "metadata": {
     "kernel": "SoS"
    },
@@ -545,7 +551,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "neither-liberty",
+   "id": "general-lewis",
    "metadata": {
     "kernel": "SoS"
    },
@@ -594,7 +600,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "needed-mitchell",
+   "id": "loving-mission",
    "metadata": {
     "kernel": "SoS"
    },
@@ -605,7 +611,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "southeast-garlic",
+   "id": "dirty-census",
    "metadata": {
     "kernel": "SoS"
    },
@@ -671,7 +677,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "driven-mills",
+   "id": "understood-motivation",
    "metadata": {
     "kernel": "SoS"
    },
@@ -686,7 +692,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "quick-windsor",
+   "id": "monthly-soccer",
    "metadata": {
     "kernel": "SoS"
    },
@@ -695,6 +701,13 @@
     "[qc_3 (export to PLINK)]\n",
     "parameter: walltime = '24h'\n",
     "parameter: remove_duplicates = False\n",
+    "# The path to the file that contains the list of samples to remove (format FID, IID)\n",
+    "parameter: remove_samples = path('.')\n",
+    "# The path to the file that contains the list of samples to keep (format FID, IID)\n",
+    "parameter: keep_samples = path('.')\n",
+    "fail_if(not (keep_samples.is_file() or keep_samples == path('.')), msg = f'Cannot find ``{keep_samples}``')\n",
+    "fail_if(not (remove_samples.is_file() or remove_samples == path('.')), msg = f'Cannot find ``{remove_samples}``')\n",
+    "\n",
     "output: f'{_input:nn}.bed'\n",
     "task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output:bn}'\n",
     "bash: container = container, expand= \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', entrypoint=entrypoint\n",
@@ -703,6 +716,8 @@
     "        --vcf-require-gt \\\n",
     "        --allow-extra-chr \\\n",
     "        --geno-counts  \\\n",
+    "        ${('--keep %s' % keep_samples) if keep_samples.is_file() else \"\"} \\\n",
+    "        ${('--remove %s' % remove_samples) if remove_samples.is_file() else \"\"} \\\n",
     "        --make-bed --out ${_output:n}  ${\"--rm-dup exclude-all\" if remove_duplicates else \"\" }\n",
     "bash: expand= \"${ }\", stderr = f'{_output:n}.stderr', stdout = f'{_output:n}.stdout', container = container, entrypoint=entrypoint\n",
     "            stdout=${_output:n}.stdout\n",
@@ -715,7 +730,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "still-basketball",
+   "id": "convertible-massage",
    "metadata": {
     "kernel": "SoS"
    },

diff --git a/code/data_preprocessing/genotype/VCF_QC.html b/code/data_preprocessing/genotype/VCF_QC.html
@@ -913,6 +913,12 @@ <h2>Command Interface<a class="headerlink" href="#command-interface" title="Perm
   qc_3:
     Workflow Options:
       --[no-]remove-duplicates (default to False)
+      --remove-samples . (as path)
+                        The path to the file that contains the list of samples
+                        to remove (format FID, IID)
+      --keep-samples . (as path)
+                        The path to the file that contains the list of samples
+                        to keep (format FID, IID)
   qc_4:
 </pre></div>
 </div>
@@ -1166,6 +1172,13 @@ <h2>Genotype QC<a class="headerlink" href="#genotype-qc" title="Permalink to thi
 <div class="highlight-sos notranslate"><div class="highlight"><pre><span></span><span class="p">[</span><span class="n">qc_3</span> <span class="p">(</span><span class="n">export</span> <span class="n">to</span> <span class="n">PLINK</span><span class="p">)]</span>
 <span class="kn">parameter:</span> <span class="kp">walltime</span> <span class="o">=</span> <span class="s1">&#39;24h&#39;</span>
 <span class="kn">parameter:</span> <span class="n">remove_duplicates</span> <span class="o">=</span> <span class="kc">False</span>
+<span class="c1"># The path to the file that contains the list of samples to remove (format FID, IID)</span>
+<span class="kn">parameter:</span> <span class="n">remove_samples</span> <span class="o">=</span> <span class="n">path</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)</span>
+<span class="c1"># The path to the file that contains the list of samples to keep (format FID, IID)</span>
+<span class="kn">parameter:</span> <span class="n">keep_samples</span> <span class="o">=</span> <span class="n">path</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)</span>
+<span class="n">fail_if</span><span class="p">(</span><span class="ow">not</span> <span class="p">(</span><span class="n">keep_samples</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="ow">or</span> <span class="n">keep_samples</span> <span class="o">==</span> <span class="n">path</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)),</span> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;Cannot find ``</span><span class="si">{</span><span class="n">keep_samples</span><span class="si">}</span><span class="s1">``&#39;</span><span class="p">)</span>
+<span class="n">fail_if</span><span class="p">(</span><span class="ow">not</span> <span class="p">(</span><span class="n">remove_samples</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="ow">or</span> <span class="n">remove_samples</span> <span class="o">==</span> <span class="n">path</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)),</span> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;Cannot find ``</span><span class="si">{</span><span class="n">remove_samples</span><span class="si">}</span><span class="s1">``&#39;</span><span class="p">)</span>
+
 <span class="kn">output:</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">_input</span><span class="si">:</span><span class="s1">nn</span><span class="si">}</span><span class="s1">.bed&#39;</span>
 <span class="kn">task:</span> <span class="kp">trunk_workers</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="kp">trunk_size</span> <span class="o">=</span> <span class="n">job_size</span><span class="p">,</span> <span class="kp">walltime</span> <span class="o">=</span> <span class="kp">walltime</span><span class="p">,</span> <span class="kp">mem</span> <span class="o">=</span> <span class="kp">mem</span><span class="p">,</span> <span class="kp">cores</span> <span class="o">=</span> <span class="n">numThreads</span><span class="p">,</span> <span class="kp">tags</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">step_name</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">_output</span><span class="si">:</span><span class="s1">bn</span><span class="si">}</span><span class="s1">&#39;</span>
 <span class="kn">bash:</span> <span class="n">container</span> <span class="o">=</span> <span class="n">container</span><span class="p">,</span> <span class="n">expand</span><span class="o">=</span> <span class="s2">&quot;${ }&quot;</span><span class="p">,</span> <span class="n">stderr</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">_output</span><span class="si">:</span><span class="s1">n</span><span class="si">}</span><span class="s1">.stderr&#39;</span><span class="p">,</span> <span class="n">stdout</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">_output</span><span class="si">:</span><span class="s1">n</span><span class="si">}</span><span class="s1">.stdout&#39;</span><span class="p">,</span> <span class="n">entrypoint</span><span class="o">=</span><span class="n">entrypoint</span>
@@ -1174,6 +1187,8 @@ <h2>Genotype QC<a class="headerlink" href="#genotype-qc" title="Permalink to thi
         <span class="o">--</span><span class="n">vcf</span><span class="o">-</span><span class="n">require</span><span class="o">-</span><span class="n">gt</span> \
         <span class="o">--</span><span class="n">allow</span><span class="o">-</span><span class="n">extra</span><span class="o">-</span><span class="nb">chr</span> \
         <span class="o">--</span><span class="n">geno</span><span class="o">-</span><span class="n">counts</span>  \
+        <span class="err">$</span><span class="p">{(</span><span class="s1">&#39;--keep </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">keep_samples</span><span class="p">)</span> <span class="k">if</span> <span class="n">keep_samples</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="k">else</span> <span class="s2">&quot;&quot;</span><span class="p">}</span> \
+        <span class="err">$</span><span class="p">{(</span><span class="s1">&#39;--remove </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">remove_samples</span><span class="p">)</span> <span class="k">if</span> <span class="n">remove_samples</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="k">else</span> <span class="s2">&quot;&quot;</span><span class="p">}</span> \
         <span class="o">--</span><span class="n">make</span><span class="o">-</span><span class="n">bed</span> <span class="o">--</span><span class="n">out</span> <span class="err">$</span><span class="p">{</span><span class="n">_output</span><span class="p">:</span><span class="n">n</span><span class="p">}</span>  <span class="err">$</span><span class="p">{</span><span class="s2">&quot;--rm-dup exclude-all&quot;</span> <span class="k">if</span> <span class="n">remove_duplicates</span> <span class="k">else</span> <span class="s2">&quot;&quot;</span> <span class="p">}</span>
 <span class="kn">bash:</span> <span class="n">expand</span><span class="o">=</span> <span class="s2">&quot;${ }&quot;</span><span class="p">,</span> <span class="n">stderr</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">_output</span><span class="si">:</span><span class="s1">n</span><span class="si">}</span><span class="s1">.stderr&#39;</span><span class="p">,</span> <span class="n">stdout</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">_output</span><span class="si">:</span><span class="s1">n</span><span class="si">}</span><span class="s1">.stdout&#39;</span><span class="p">,</span> <span class="n">container</span> <span class="o">=</span> <span class="n">container</span><span class="p">,</span> <span class="n">entrypoint</span><span class="o">=</span><span class="n">entrypoint</span>
             <span class="n">stdout</span><span class="o">=</span><span class="err">$</span><span class="p">{</span><span class="n">_output</span><span class="p">:</span><span class="n">n</span><span class="p">}</span><span class="o">.</span><span class="n">stdout</span>

diff --git a/searchindex.js b/searchindex.js