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index.html

@@ -228,6 +228,17 @@
 
 
 
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+
+
+  <span class="md-ellipsis">
+    Readme
+  </span>
+
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+
       <a href="." class="md-nav__link md-nav__link--active">
 
 
@@ -238,6 +249,61 @@
 
       </a>
 
+
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+
+
+
+
+
+
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+
+        <li class="md-nav__item">
+  <a href="#install" class="md-nav__link">
+    <span class="md-ellipsis">
+      install
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#login" class="md-nav__link">
+    <span class="md-ellipsis">
+      login
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#search" class="md-nav__link">
+    <span class="md-ellipsis">
+      search
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#download" class="md-nav__link">
+    <span class="md-ellipsis">
+      download
+    </span>
+  </a>
+
+</li>
+
+    </ul>
+
+</nav>
+
     </li>
 
 
@@ -282,6 +348,50 @@
 
 
 
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+
+        <li class="md-nav__item">
+  <a href="#install" class="md-nav__link">
+    <span class="md-ellipsis">
+      install
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#login" class="md-nav__link">
+    <span class="md-ellipsis">
+      login
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#search" class="md-nav__link">
+    <span class="md-ellipsis">
+      search
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#download" class="md-nav__link">
+    <span class="md-ellipsis">
+      download
+    </span>
+  </a>
+
+</li>
+
+    </ul>
+
 </nav>
                   </div>
                 </div>
@@ -299,7 +409,33 @@
 
 
 <h1 id="gisflu">gisflu</h1>
-<p>Access the GISAID Flu database using Python</p>
+<p>Access the GISAID Flu database using Python. Inspired by <a href="https://github.com/Wytamma/GISAIDR/tree/master">GISAIDR</a>, which is an R package for accessing the EpiCoV, EpiRSV and EpiPox database of GISAID.</p>
+<h2 id="install">install</h2>
+<pre><code class="language-sh"># use pip
+pip install gisflu
+# use pdm
+pdm add gisflu
+</code></pre>
+<h2 id="login">login</h2>
+<pre><code class="language-python">import gisflu
+
+# Log in with provided username and password
+gisflu.login(&quot;myusername&quot;, &quot;mypassword&quot;)
+
+# Log in using environment variables
+gisflu.login()
+</code></pre>
+<h2 id="search">search</h2>
+<pre><code class="language-python">cred = gisflu.login()
+gisflu.search(cred, type=[&quot;A&quot;], HA=[&quot;3&quot;], NA=[&quot;2&quot;],
+    collectDateFrom=&quot;2020-01-01&quot;, recordLimit=10)
+</code></pre>
+<h2 id="download">download</h2>
+<pre><code class="language-python">cred = gisflu.login()
+isolateIds = [&quot;EPI_ISL_19185107&quot;, &quot;EPI_ISL_19151100&quot;]
+gisflu.download(cred, isolateIds, downloadType=&quot;protein&quot;, segments=[&quot;HA&quot;, &quot;NA&quot;],
+    filename=&quot;records.fasta&quot;)
+</code></pre>
 
 
 

sitemap.xml

@@ -5,6 +5,11 @@
          <lastmod>2024-06-25</lastmod>
          <changefreq>daily</changefreq>
     </url>
+    <url>
+         <loc>https://william-swl.github.io/gisflu/dev/</loc>
+         <lastmod>2024-06-25</lastmod>
+         <changefreq>daily</changefreq>
+    </url>
     <url>
          <loc>https://william-swl.github.io/gisflu/reference/</loc>
          <lastmod>2024-06-25</lastmod>