v0.17.0

shenwei356 · Jul 3, 2024 · 0132a50 · 0132a50
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diff --git a/download/index.html b/download/index.html
@@ -661,19 +661,22 @@ <h1 id="download">Download<a class="headerlink" href="#download" title="Permanen
   in <a href="https://github.com/shenwei356/taxonkit/releases">release</a> page.</p>
 <h2 id="current-version">Current Version<a class="headerlink" href="#current-version" title="Permanent link">Link</a></h2>
 <ul>
-<li><a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0">TaxonKit v0.16.0</a>
-<a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.0/total.svg" /></a><ul>
-<li><code>taxonkit create-taxdump</code>:<ul>
-<li>TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). <a href="https://github.com/shenwei356/taxonkit/issues/92">#92</a>.</li>
+<li><a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.17.0">TaxonKit v0.17.0</a>
+<a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.17.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.17.0/total.svg" /></a><ul>
+<li><code>taxonkit filter</code>:<ul>
+<li>Fix keeping taxids with a rank of "no rank" or "clade". <a href="https://github.com/shenwei356/taxonkit/issues/97">#97</a></li>
 </ul>
 </li>
-<li><code>taxonkit taxid-changelog/create-taxdump</code>:<ul>
-<li>Add notes about the possible error records in taxid-changelog built from taxonomic data created by <code>create-taxdump</code>. <a href="https://github.com/shenwei356/taxonkit/issues/91">#91</a></li>
-<li>Dont't worry, a single version of taxonomic data created by <code>taxonkit create-taxdump</code> has no problem, it's just the changelog might not be perfect.</li>
+<li><code>taxonkit list</code>:<ul>
+<li>Accept input TaxIds from stdin/files, not just the flag <code>--ids</code>. <a href="https://github.com/shenwei356/taxonkit/issues/93">#93</a></li>
 </ul>
 </li>
-<li><code>taxonkit lca</code>:<ul>
-<li>new flag <code>-K/--keep-invalid</code>: print the query even if no single valid taxid left. <a href="https://github.com/shenwei356/taxonkit/issues/89">#89</a></li>
+<li><code>taxonkit name2taxid</code>:<ul>
+<li>Add support of fuzzy match with <code>-f/--fuzzy</code>. <a href="https://github.com/shenwei356/taxonkit/issues/88">#88</a></li>
+</ul>
+</li>
+<li><code>taxonkit profile2cami</code>:<ul>
+<li>Add a new flag <code>-S/--no-sum-up</code> to disable summing up abundances. <a href="https://github.com/shenwei356/taxonkit/issues/99">#99</a></li>
 </ul>
 </li>
 </ul>
@@ -703,32 +706,32 @@ <h3 id="links">Links<a class="headerlink" href="#links" title="Permanent link">L
 <tr>
 <td style="text-align: left;">Linux</td>
 <td style="text-align: left;"><strong>64-bit</strong></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_amd64.tar.gz"><strong>taxonkit_linux_amd64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_amd64.tar.gz"><strong>taxonkit_linux_amd64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 <tr>
 <td style="text-align: left;">Linux</td>
 <td style="text-align: left;"><strong>arm64</strong></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_arm64.tar.gz"><strong>taxonkit_linux_arm64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_arm64.tar.gz"><strong>taxonkit_linux_arm64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 <tr>
 <td style="text-align: left;">macOS</td>
 <td style="text-align: left;"><strong>64-bit</strong></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_amd64.tar.gz"><strong>taxonkit_darwin_amd64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_amd64.tar.gz"><strong>taxonkit_darwin_amd64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 <tr>
 <td style="text-align: left;">macOS</td>
 <td style="text-align: left;"><strong>arm64</strong></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_arm64.tar.gz"><strong>taxonkit_darwin_arm64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_arm64.tar.gz"><strong>taxonkit_darwin_arm64.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 <tr>
 <td style="text-align: left;">Windows</td>
 <td style="text-align: left;"><strong>64-bit</strong></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_windows_amd64.exe.tar.gz"><strong>taxonkit_windows_amd64.exe.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_windows_amd64.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_windows_amd64.exe.tar.gz"><strong>taxonkit_windows_amd64.exe.tar.gz</strong></a>,<br/> <a href="http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_windows_amd64.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 </tbody>
 </table>
@@ -858,6 +861,23 @@ <h2 id="dataset">Dataset<a class="headerlink" href="#dataset" title="Permanent l
 <p><strong>Update dataset</strong>: Simply re-download the taxdump files, uncompress and override old ones.</p>
 <h2 id="release-history">Release history<a class="headerlink" href="#release-history" title="Permanent link">Link</a></h2>
 <ul>
+<li><a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0">TaxonKit v0.16.0</a>
+<a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.0/total.svg" /></a><ul>
+<li><code>taxonkit create-taxdump</code>:<ul>
+<li>TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). <a href="https://github.com/shenwei356/taxonkit/issues/92">#92</a>.</li>
+</ul>
+</li>
+<li><code>taxonkit taxid-changelog/create-taxdump</code>:<ul>
+<li>Add notes about the possible error records in taxid-changelog built from taxonomic data created by <code>create-taxdump</code>. <a href="https://github.com/shenwei356/taxonkit/issues/91">#91</a></li>
+<li>Dont't worry, a single version of taxonomic data created by <code>taxonkit create-taxdump</code> has no problem, it's just the changelog might not be perfect.</li>
+</ul>
+</li>
+<li><code>taxonkit lca</code>:<ul>
+<li>new flag <code>-K/--keep-invalid</code>: print the query even if no single valid taxid left. <a href="https://github.com/shenwei356/taxonkit/issues/89">#89</a></li>
+</ul>
+</li>
+</ul>
+</li>
 <li><a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.15.1">TaxonKit v0.15.1</a>
 <a href="https://github.com/shenwei356/taxonkit/releases/tag/v0.15.1"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.15.1/total.svg" /></a><ul>
 <li><code>taxonkit name2taxid</code>:<ul>

diff --git a/search/search_index.json b/search/search_index.json
diff --git a/sitemap.xml b/sitemap.xml
@@ -2,42 +2,42 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/bioinf/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/chinese-dev/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/chinese/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/download/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/tutorial/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/usage/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://bioinf.shenwei.me/taxonkit/bench/</loc>
-         <lastmod>2024-04-11</lastmod>
+         <lastmod>2024-07-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
 </urlset>
diff --git a/sitemap.xml.gz b/sitemap.xml.gz