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nvelden / geneviewer

An R package designed for drawing gene arrow maps
https://nvelden.github.io/geneviewer/
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Having problem with import some specific .gbk files #3

Closed yamn29302 closed 5 months ago

yamn29302 commented 5 months ago

Hi,

Thanks for developing this sweet package saving me lots of time playing with powerpoint. I have encountered a problem with some specific .gbk files downloaded directly from GenBank. More specifically, it has something to do with read_gbk() function. Most of the files I have can be transformed into df perfectly. However I've got 2 files can't be parsed by read_gbk() as expected. The "FEATURES" of the resulting list is somehow going wrong which I can't fix. 螢幕擷取畫面 2024-04-20 141412

The .gbk files are uploaded onto google drive. The link is provided below. https://drive.google.com/drive/folders/1CRT8u6T_U8YflGqzbC5uwfq7dVfKBtyt?usp=drive_link

nvelden commented 5 months ago

The supplied GenBank files contain genomic data for multiple loci, each separated by "//" and with its own FEATURES section. The function will only read the FEATURES from the first locus. To access all information, either split each locus into a separate GenBank file or identify and load only the locus containing your gene of interest.

yamn29302 commented 5 months ago

Many thanks to your reply!! The finction works perfectly after I split the .gbk file into mutiple files. The splitting script I used is below. (change .txt to .sh and worked under linux environment) split.txt