stitchr
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JamieHeather
Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info
Currently when submitting a rearrangements using nucleotide CDR3s, Stitchr will produce a small proportion of TCRs where the stitched nucleotide sequence does not exactly replicate the sequence that appeared in...
Currently `stitchr` uses Kasuza frequency data to pick codons for residues that are not wholly germline-encodable when providing AA CDRs. This basically picks the most common nucleotide triplet used from...
Currently it's awkward to add additional genes, both due to having to confirm to the altered IMGT header format and locating the relevant file in the squirreled away data directory....
Using 'TRAVx*%' in Thimble _should_ produce rows in the output for that rearrangement with all included alleles of TRAVx, however it currently only includes alleles that are included in the...
Even if properly present and correct, leader sequences aren't being detected.
Also needs to infer and handle D genes better, if only to state it's skipping
Would you be open to switching from PySimpleGUI to tkinter (or something else)? We've had a tough time with the PySimpleGUI licensing changes and now it seems the package is...
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Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info