2025-06-24: v1.3.1, fixes #49 (inappropriate divisible by 3 warning)

Author: JamieHeather

docs/_build/doctrees/environment.pickle

@@ -1,4 +1,4 @@
-.. stitchr documentation master file, created by
+.. stitchr documentation master file, first created by
    sphinx-quickstart on Tue Apr 18 16:30:31 2023.
 
 stitchr
@@ -33,8 +33,8 @@ The script takes the known V/J/CDR3 information, and uses that to pull out the r
 
 Out of the box, ``stitchr`` works on all common jawed vertebrate TCR loci (alpha/beta/gamma/delta), for all species for which there is currently data available in IMGT.
 
-What's new in v1.3.0
-====================
+What's new in v1.3
+==================
 
 (2025-04-25)
 
@@ -46,8 +46,8 @@ A couple of minor case use capabilities have been added in this version.
 
 * In order to simplify tracking of different ``stitchr`` updates, script-specific versions have been removed and updates are tracked wholly through package-level versioning. This can be easily obtained by running the ``--version`` option in any of the command scripts, or ``--cite`` for a fuller description.
 
-What's new in v1.2.0
-====================
+What's new in v1.2
+==================
 
 (2025-02-24)
 

docs/_build/doctrees/index.doctree

@@ -38,7 +38,7 @@ For human and mouse TCRs, the script will use the TRBC gene located in the same
 Translation sequences
 ---------------------
 
-By default ``stitchr`` does not include stop codons at the end of the coding sequence; if desired, this must be specified using the 3' flag (``-3p``), i.e. ``-3p TAA``, ``-3p TAG``, or ``-3p TGA``. Similarly, no sequence is included before that of the IMGT-recorded L1 leader sequence. If desired, this can be added using the 5' flag (``-5p``), e.g. to add the pre-start codon section of an optimal Kozak sequence: ``-5p GCCGCCACC``. Note that translated sequence in the output is the *whole* stitched sequence, including any added 5'/3' sequences: addition of 5' sequences may cause the introduction of underscores (`\_') to appear in the translated output, representing incomplete codons that could not be translated. Also note that the translated sequence of an individual chain may differ from the corresponding section of a linked heterodimer for this reason, depending on the length/frame of the 5' rearrangement.
+By default ``stitchr`` does not include stop codons at the end of the coding sequence; if desired, this must be specified using the 3' flag (``-3p``), i.e. ``-3p TAA``, ``-3p TAG``, or ``-3p TGA``. Similarly, no sequence is included before that of the IMGT-recorded L1 leader sequence. If desired, this can be added using the 5' flag (``-5p``), e.g. to add the pre-start codon section of an optimal Kozak sequence: ``-5p GCCGCCACC``. Note that translated sequence in the output is the *whole* stitched sequence, including any added 5'/3' sequences: addition of 5' sequences may cause the introduction of underscores to appear in the translated output, representing incomplete codons that could not be translated. Also note that the translated sequence of an individual chain may differ from the corresponding section of a linked heterodimer for this reason, depending on the length/frame of the 5' rearrangement.
 
 Seamless mode
 -------------

docs/_build/doctrees/usage.doctree

@@ -132,8 +132,8 @@ <h2>Stitch together TCR coding nucleotide sequences from V/J/CDR3 information<a
 <p>Out of the box, <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> works on all common jawed vertebrate TCR loci (alpha/beta/gamma/delta), for all species for which there is currently data available in IMGT.</p>
 </section>
 </section>
-<section id="what-s-new-in-v1-3-0">
-<h1>What’s new in v1.3.0<a class="headerlink" href="#what-s-new-in-v1-3-0" title="Link to this heading"></a></h1>
+<section id="what-s-new-in-v1-3">
+<h1>What’s new in v1.3<a class="headerlink" href="#what-s-new-in-v1-3" title="Link to this heading"></a></h1>
 <p>(2025-04-25)</p>
 <p>A couple of minor case use capabilities have been added in this version.</p>
 <ul class="simple">
@@ -142,8 +142,8 @@ <h1>What’s new in v1.3.0<a class="headerlink" href="#what-s-new-in-v1-3-0" tit
 <li><p>In order to simplify tracking of different <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> updates, script-specific versions have been removed and updates are tracked wholly through package-level versioning. This can be easily obtained by running the <code class="docutils literal notranslate"><span class="pre">--version</span></code> option in any of the command scripts, or <code class="docutils literal notranslate"><span class="pre">--cite</span></code> for a fuller description.</p></li>
 </ul>
 </section>
-<section id="what-s-new-in-v1-2-0">
-<h1>What’s new in v1.2.0<a class="headerlink" href="#what-s-new-in-v1-2-0" title="Link to this heading"></a></h1>
+<section id="what-s-new-in-v1-2">
+<h1>What’s new in v1.2<a class="headerlink" href="#what-s-new-in-v1-2" title="Link to this heading"></a></h1>
 <p>(2025-02-24)</p>
 <p>There are a number of minor tweaks and quality of life improvements in the update from version 1.1.3 to 1.2.0, with the major changes aiming to improve repeatability and user convenience, including:</p>
 <ul>

docs/_build/html/_sources/index.rst.txt

@@ -122,7 +122,7 @@ <h2>Gene/allele default behaviour<a class="headerlink" href="#gene-allele-defaul
 </section>
 <section id="translation-sequences">
 <h2>Translation sequences<a class="headerlink" href="#translation-sequences" title="Link to this heading"></a></h2>
-<p>By default <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> does not include stop codons at the end of the coding sequence; if desired, this must be specified using the 3’ flag (<code class="docutils literal notranslate"><span class="pre">-3p</span></code>), i.e. <code class="docutils literal notranslate"><span class="pre">-3p</span> <span class="pre">TAA</span></code>, <code class="docutils literal notranslate"><span class="pre">-3p</span> <span class="pre">TAG</span></code>, or <code class="docutils literal notranslate"><span class="pre">-3p</span> <span class="pre">TGA</span></code>. Similarly, no sequence is included before that of the IMGT-recorded L1 leader sequence. If desired, this can be added using the 5’ flag (<code class="docutils literal notranslate"><span class="pre">-5p</span></code>), e.g. to add the pre-start codon section of an optimal Kozak sequence: <code class="docutils literal notranslate"><span class="pre">-5p</span> <span class="pre">GCCGCCACC</span></code>. Note that translated sequence in the output is the <em>whole</em> stitched sequence, including any added 5’/3’ sequences: addition of 5’ sequences may cause the introduction of underscores (<a href="#id1"><span class="problematic" id="id2">`</span></a>_’) to appear in the translated output, representing incomplete codons that could not be translated. Also note that the translated sequence of an individual chain may differ from the corresponding section of a linked heterodimer for this reason, depending on the length/frame of the 5’ rearrangement.</p>
+<p>By default <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> does not include stop codons at the end of the coding sequence; if desired, this must be specified using the 3’ flag (<code class="docutils literal notranslate"><span class="pre">-3p</span></code>), i.e. <code class="docutils literal notranslate"><span class="pre">-3p</span> <span class="pre">TAA</span></code>, <code class="docutils literal notranslate"><span class="pre">-3p</span> <span class="pre">TAG</span></code>, or <code class="docutils literal notranslate"><span class="pre">-3p</span> <span class="pre">TGA</span></code>. Similarly, no sequence is included before that of the IMGT-recorded L1 leader sequence. If desired, this can be added using the 5’ flag (<code class="docutils literal notranslate"><span class="pre">-5p</span></code>), e.g. to add the pre-start codon section of an optimal Kozak sequence: <code class="docutils literal notranslate"><span class="pre">-5p</span> <span class="pre">GCCGCCACC</span></code>. Note that translated sequence in the output is the <em>whole</em> stitched sequence, including any added 5’/3’ sequences: addition of 5’ sequences may cause the introduction of underscores to appear in the translated output, representing incomplete codons that could not be translated. Also note that the translated sequence of an individual chain may differ from the corresponding section of a linked heterodimer for this reason, depending on the length/frame of the 5’ rearrangement.</p>
 </section>
 <section id="seamless-mode">
 <h2>Seamless mode<a class="headerlink" href="#seamless-mode" title="Link to this heading"></a></h2>

docs/_build/html/_sources/usage.rst.txt

@@ -33,8 +33,8 @@ The script takes the known V/J/CDR3 information, and uses that to pull out the r
 
 Out of the box, ``stitchr`` works on all common jawed vertebrate TCR loci (alpha/beta/gamma/delta), for all species for which there is currently data available in IMGT.
 
-What's new in v1.3.0
-====================
+What's new in v1.3
+==================
 
 (2025-04-25)
 
@@ -46,8 +46,8 @@ A couple of minor case use capabilities have been added in this version.
 
 * In order to simplify tracking of different ``stitchr`` updates, script-specific versions have been removed and updates are tracked wholly through package-level versioning. This can be easily obtained by running the ``--version`` option in any of the command scripts, or ``--cite`` for a fuller description.
 
-What's new in v1.2.0
-====================
+What's new in v1.2
+==================
 
 (2025-02-24)
 

docs/_build/html/index.html

@@ -1,6 +1,6 @@
 [metadata]
 name = stitchr
-version = 1.3.0
+version = 1.3.1
 author = Jamie Heather
 author_email = jheather@mgh.harvard.edu
 description = Stitch together coding TCR sequences from V/J/CDR3 information