[question] how to add a gene track as displayed in the 'introduction'?

[JWDebler]

Hi, I'd like to add a 'Gene' track the way it is displayed in the Introduction section:

But I can't figure out what tags in the 'tracks.txt' file to use to make it look like that. I can only get it to look like the 'SNP' track. Cheers

[mnshgl0110]

Hi Johannes, you have to use ft:gff and a GFF file to plot genes. Please check the example track file. Best Manish

[JWDebler]

How exactly does plotsr expect a gff file to be formated like? I converted mine into a bed file as I would just get gff parsing errors.

track - WARNING - Reading GFF file AlKewell_EC_fixed_CDS_added_NCBI-ready.gff3. Overlapping transcripts would be plotted as such without any filtering.
Traceback (most recent call last):
  File "/home/ubuntu/miniconda3/envs/plotsr/bin/plotsr", line 6, in <module>
    main(sys.argv[1:])
  File "/home/ubuntu/miniconda3/envs/plotsr/lib/python3.10/site-packages/plotsr/main.py", line 55, in main
    plotsr(args)
  File "/home/ubuntu/miniconda3/envs/plotsr/lib/python3.10/site-packages/plotsr/plotsr.py", line 257, in plotsr
    tracks = readtrack(TRACKS, chrlengths)
  File "/home/ubuntu/miniconda3/envs/plotsr/lib/python3.10/site-packages/plotsr/func.py", line 732, in readtrack
    t.readdata(chrlengths)
  File "/home/ubuntu/miniconda3/envs/plotsr/lib/python3.10/site-packages/plotsr/func.py", line 702, in readdata
    self._readgff(chrlengths)
  File "/home/ubuntu/miniconda3/envs/plotsr/lib/python3.10/site-packages/plotsr/func.py", line 657, in _readgff
    if line[0] not in chrs:
IndexError: list index out of range

[mnshgl0110]

There is an example gff file (and other example data) here. Are there empty lines in the GFF? They would result in this error. Removing them should fix it.

[JWDebler]

Hi, I found the problem. There was an empty line as the last line in my gff3. That took some time to pick up :-)