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Note that the ``stitch`` function returns a nested dictionary, containing various levels that relate to information about the rearrangement in question at different stages of its handling. These fields are described in the :ref:`output-label` page (although note that the raw ``stitch()`` function output is only a subset of the fields described there, as the individual scripts each add additional data post-stitching.
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@@ -33,9 +33,24 @@ The script takes the known V/J/CDR3 information, and uses that to pull out the r
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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.
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What's new in v1.3.0
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====================
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(2025-04-25)
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A couple of minor case use capabilities have been added in this version.
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* A ``-nl / --no_leader`` flag has been added, so that TCRs can be generated without a leader region (as `had been requested in the Issues page <https://github.com/JamieHeather/stitchr/issues/45>`_). Note that this option should be avoided for construction TCR sequences for functional expression, as these regions encode the signal peptide and are thus required for proper polypeptide trafficking.
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* A ``-sn / --skip_n_checks`` flag has been added, allowing the production of `TCRs with CDR3 junctions which do not begin with the classical conserved second cysteine <https://github.com/JamieHeather/stitchr/issues/46>`_ when providing exact CDR3 junctions. Note that this option will only work for rearrangements which have deleted this CYS104 residue; in the absence of any N-terminal overlap (which previously was the Cys as a minimum), it now places the provided junction sequence with the first CDR3 residue in place of CYS104. (The only way to get ``stitchr`` to reliably produce rearrangements which have deleted beyond this position is to provide nucleotide sequence which extends further into the V region, in conjunction with the ``-sl / --seamless`` flag.)
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* 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.
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What's new in v1.2.0
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====================
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(2025-02-24)
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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:
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* ``stitchr`` has changed how it stores and handles data, as laid out in the :ref:`output-label` section...
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* `stitchr on PyPI <https://pypi.org/project/stitchr/>`_
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Translation sequences
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---------------------
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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.
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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.
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Seamless mode
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-------------
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- ``-m`` - define an output mode, to define which sequences get printed to the terminal
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- ``-xg`` - toggle providing additional/custom genes to be stitched into TCR transcripts in the Data/additional-genes.fasta file
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- ``-sc`` - toggle skipping the constant region gene check (for genes not present in the C-region-motifs.tsv file)
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- ``-sn`` - `toggle skipping the CDR3 N terminal check, allowing for the stitching of TCR rearrangements that have deleted the junction-defining conserved second cysteine residue <https://github.com/JamieHeather/stitchr/issues/46>`_
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- ``-nl`` - allow for produc
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- ``-sw`` - suppress warning text, which may be especially useful in conjunction with some of the alternative output modes (see the :ref:`output-label` section)
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