v2.10.1

Author: shenwei356

download/index.html

@@ -628,27 +628,30 @@ <h1 id="download">Download</h1>
 <span class="__dimensions_badge_embed__" data-doi="10.1002/imt2.191" data-style="small_rectangle"></span></p>
 <h2 id="current-version">Current Version</h2>
 <ul>
-<li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.10.0">SeqKit v2.10.0</a> - 2025-03-12
-<a href="https://github.com/shenwei356/seqkit/releases/tag/v2.10.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.10.0/total.svg" /></a><ul>
-<li><code>seqkit</code>:<ul>
-<li>add a global flag <code>--skip-file-check</code>: skip input file checking when given a file list if you believe these files do exist.
-It helps to reduce file checking time when given a huge number of sequence files.</li>
+<li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.10.1">SeqKit v2.10.1</a> - 2025-08-19
+<a href="https://github.com/shenwei356/seqkit/releases/tag/v2.10.1"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.10.1/total.svg" /></a><ul>
+<li><code>seqkit seq</code>:<ul>
+<li>fix validating sequences: it failed to report an error when the invalid sequence is not the last one in the input. <a href="https://github.com/shenwei356/seqkit/issues/536">#536</a></li>
 </ul>
 </li>
-<li><code>seqkit split2</code>:<ul>
-<li>fix prefix checking when paired-end files are given. <a href="https://github.com/shenwei356/seqkit/issues/512">#512</a></li>
+<li><code>seqkit stats</code>:<ul>
+<li>fix decimal places of some fields when using <code>-T</code>.</li>
 </ul>
 </li>
-<li><code>seqkit stat</code>:<ul>
-<li>do not compute GC content and N's for protein sequence. <a href="https://github.com/shenwei356/seqkit/issues/497">#497</a></li>
+<li><code>seqkit fx2tab</code>:<ul>
+<li>fix the calculation of GC content (<code>--gc</code>). Previously, the denominator was the total sequence length, which could lead to inaccuracies due to the potential presence of gaps in the sequence. <a href="https://github.com/shenwei356/seqkit/issues/515">#515</a></li>
 </ul>
 </li>
-<li><code>seqkit grep</code>:<ul>
-<li>add early exit for <code>--delete-matched</code> when no patterns remain <a href="https://github.com/shenwei356/seqkit/pull/505">#505</a> by @sawyerknoblich</li>
+<li><code>seqkit sample</code>:<ul>
+<li>fix <code>-n</code> for in-memory mode. <a href="https://github.com/shenwei356/seqkit/issues/518">#518</a></li>
 </ul>
 </li>
-<li><code>seqkit concat</code>:<ul>
-<li>add an option <code>-F/--fill</code> to use a sequence of "-" for IDs missing in some files, can be used in MSA results. <a href="https://github.com/shenwei356/seqkit/issues/510">#510</a></li>
+<li><code>seqkit subseq</code>:<ul>
+<li>fix the bug that subseq --feature is not case insensitive. <a href="https://github.com/shenwei356/seqkit/issues/523">#523</a></li>
+</ul>
+</li>
+<li><code>seqkit grep/locate/mutate</code>:<ul>
+<li>update help message for <code>-p/--pattern</code>, to show how to set multiple values. <a href="https://github.com/shenwei356/seqkit/pull/527">#527</a> by @corneliusroemer</li>
 </ul>
 </li>
 </ul>
@@ -668,50 +671,50 @@ <h3 id="links">Links</h3>
 <tr>
 <td style="text-align: left;">Linux</td>
 <td style="text-align: left;">32-bit</td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_linux_386.tar.gz">seqkit_linux_386.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_linux_386.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_386.tar.gz">seqkit_linux_386.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_386.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 <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/seqkit/releases/download/v2.10.0/seqkit_linux_amd64.tar.gz"><strong>seqkit_linux_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_linux_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_amd64.tar.gz"><strong>seqkit_linux_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_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/seqkit/releases/download/v2.10.0/seqkit_linux_arm64.tar.gz"><strong>seqkit_linux_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_linux_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_arm64.tar.gz"><strong>seqkit_linux_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_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/seqkit/releases/download/v2.10.0/seqkit_darwin_amd64.tar.gz"><strong>seqkit_darwin_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_darwin_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_darwin_amd64.tar.gz"><strong>seqkit_darwin_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_darwin_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_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/seqkit/releases/download/v2.10.0/seqkit_darwin_arm64.tar.gz"><strong>seqkit_darwin_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_darwin_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_darwin_arm64.tar.gz"><strong>seqkit_darwin_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_darwin_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 <tr>
 <td style="text-align: left;">Windows</td>
 <td style="text-align: left;">32-bit</td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_windows_386.exe.tar.gz">seqkit_windows_386.exe.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_windows_386.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_windows_386.exe.tar.gz">seqkit_windows_386.exe.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_windows_386.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.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/seqkit/releases/download/v2.10.0/seqkit_windows_amd64.exe.tar.gz"><strong>seqkit_windows_amd64.exe.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz">中国镜像</a></td>
-<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.0/seqkit_windows_amd64.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600" /></a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_windows_amd64.exe.tar.gz"><strong>seqkit_windows_amd64.exe.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz">中国镜像</a></td>
+<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_windows_amd64.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600" /></a></td>
 </tr>
 </tbody>
 </table>
 <p><em>Notes</em></p>
 <ul>
-<li>please open an issuse to request binaries for other platforms.</li>
+<li>please open an issue to request binaries for other platforms.</li>
 <li>run <code>seqkit version</code> to check update !!!</li>
 <li>run <code>seqkit genautocomplete</code> to update shell autocompletion script !!!</li>
 </ul>
@@ -765,9 +768,9 @@ <h4 id="method-6-compiling-from-source-latest-stabledev-version">Method 6: Compi
 <pre><code># ------------------- install golang -----------------
 
 # download Go from https://go.dev/dl
-wget https://go.dev/dl/go1.24.1.linux-amd64.tar.gz
+wget https://go.dev/dl/go1.25.0.linux-amd64.tar.gz
 
-tar -zxf go1.24.1.linux-amd64.tar.gz -C $HOME/
+tar -zxf go1.25.0.linux-amd64.tar.gz -C $HOME/
 
 # or 
 #   echo "export PATH=$PATH:$HOME/go/bin" &gt;&gt; ~/.bashrc
@@ -780,8 +783,9 @@ <h4 id="method-6-compiling-from-source-latest-stabledev-version">Method 6: Compi
 cd seqkit/seqkit/
 
 # optionally choose a release
-# git check v2.10.0
+# git check v2.10.1
 
+export GOEXPERIMENT=greenteagc # for go1.25
 go build -trimpath -ldflags="-s -w" -tags netgo
 
 # The executable binary file is located in:
@@ -814,6 +818,31 @@ <h2 id="shell-completion">Shell-completion</h2>
 </code></pre>
 <h2 id="release-history">Release history</h2>
 <ul>
+<li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.10.0">SeqKit v2.10.0</a> - 2025-03-12
+<a href="https://github.com/shenwei356/seqkit/releases/tag/v2.10.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.10.0/total.svg" /></a><ul>
+<li><code>seqkit</code>:<ul>
+<li>add a global flag <code>--skip-file-check</code>: skip input file checking when given a file list if you believe these files do exist.
+It helps to reduce file checking time when given a huge number of sequence files.</li>
+</ul>
+</li>
+<li><code>seqkit split2</code>:<ul>
+<li>fix prefix checking when paired-end files are given. <a href="https://github.com/shenwei356/seqkit/issues/512">#512</a></li>
+</ul>
+</li>
+<li><code>seqkit stat</code>:<ul>
+<li>do not compute GC content and N's for protein sequence. <a href="https://github.com/shenwei356/seqkit/issues/497">#497</a></li>
+</ul>
+</li>
+<li><code>seqkit grep</code>:<ul>
+<li>add early exit for <code>--delete-matched</code> when no patterns remain <a href="https://github.com/shenwei356/seqkit/pull/505">#505</a> by @sawyerknoblich</li>
+</ul>
+</li>
+<li><code>seqkit concat</code>:<ul>
+<li>add an option <code>-F/--fill</code> to use a sequence of "-" for IDs missing in some files, can be used in MSA results. <a href="https://github.com/shenwei356/seqkit/issues/510">#510</a></li>
+</ul>
+</li>
+</ul>
+</li>
 <li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.9.0">SeqKit v2.9.0</a> - 2024-11-01
 <a href="https://github.com/shenwei356/seqkit/releases/tag/v2.9.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.9.0/total.svg" /></a><ul>
 <li><code>seqkit</code>:<ul>

search/search_index.json

@@ -2910,8 +2910,9 @@ <h2 id="grep">grep</h2>
   -m, --max-mismatch int            max mismatch when matching by seq. For large genomes like human
                                     genome, using mapping/alignment tools would be faster
   -P, --only-positive-strand        only search on the positive strand
-  -p, --pattern strings             search pattern (multiple values supported. Attention: use double
-                                    quotation marks for patterns containing comma, e.g., -p '&quot;A{2,}&quot;')
+  -p, --pattern strings             search pattern. Multiple values supported: comma-separated (e.g., -p
+                                    &quot;p1,p2&quot;) OR use -p multiple times (e.g., -p p1 -p p2). Make sure to
+                                    quote literal commas, e.g. in regex patterns '&quot;A{2,}&quot;'
   -f, --pattern-file string         pattern file (one record per line)
   -R, --region string               specify sequence region for searching. e.g 1:12 for first 12 bases,
                                     -12:-1 for last 12 bases
@@ -3084,8 +3085,9 @@ <h2 id="locate">locate</h2>
                                using mapping/alignment tools would be faster
   -G, --non-greedy             non-greedy mode, faster but may miss motifs overlapping with others
   -P, --only-positive-strand   only search on positive strand
-  -p, --pattern strings        pattern/motif (multiple values supported. Attention: use double quotation
-                               marks for patterns containing comma, e.g., -p '&quot;A{2,}&quot;')
+  -p, --pattern strings        pattern/motif. Multiple values supported: comma-separated (e.g., -p
+                               &quot;p1,p2&quot;) OR use -p multiple times (e.g., -p p1 -p p2). Make sure to quote
+                               literal commas, e.g. in regex patterns '&quot;A{2,}&quot;'
   -f, --pattern-file string    pattern/motif file (FASTA format)
   -F, --use-fmi                use FM-index for much faster search of lots of sequence patterns
   -r, --use-regexp             patterns/motifs are regular expression
@@ -4764,9 +4766,9 @@ <h2 id="mutate">mutate</h2>
                               0:ACGT for inserting ACGT at the beginning, -1:* for add * to the end
   -v, --invert-match          [match seqs to mutate] invert the sense of matching, to select
                               non-matching records
-  -s, --pattern strings       [match seqs to mutate] search pattern (multiple values supported.
-                              Attention: use double quotation marks for patterns containing comma, e.g.,
-                              -p '&quot;A{2,}&quot;'))
+  -s, --pattern strings       [match seqs to mutate] search pattern .Multiple values supported:
+                              comma-separated (e.g., -p &quot;p1,p2&quot;) OR use -p multiple times (e.g., -p p1
+                              -p p2). Make sure to quote literal commas, e.g. in regex patterns '&quot;A{2,}&quot;'
   -f, --pattern-file string   [match seqs to mutate] pattern file (one record per line)
   -p, --point strings         point mutation: changing base at given position. e.g., -p 2:C for setting
                               2nd base as C, -p -1:A for change last base as A