"gt gff3 -sortlines -tidy -retainids" reduce some lines

Question

[153348734]

==> cultivar_Lee.repeat.gff3 <==,

chr1    .       Repeat  28      95      .       +       .       Name=LTR/Gypsy;Family=TE_00002776_INT

chr1    .       Repeat  222     267     .       +       .       Name=LTR/Gypsy;Family=TE_00002776_INT

chr1    .       Repeat  287     349     .       +       .       Name=LTR/Gypsy;Family=TE_00002776_INT

chr1    .       Repeat  430     472     .       +       .       Name=LTR/Gypsy;Family=TE_00002776_INT

chr1    .       Repeat  581     626     .       +       .       Name=LTR/Gypsy;Family=TE_00002776_INT

chr1    .       Repeat  646     708     .       +       .       Name=LTR/Gypsy;Family=TE_00002776_INT

chr1    .       Repeat  817     883     .       +       .       Name=LTR/Gypsy;Family=TE_00002776_INT

==> cultivar_Lee.repeat.sorted.gff3 <==

chr1    .       Repeat  2808    2875    .       +       .       Name=LTR/Gypsy;family=TE_00002776_INT

chr1    .       Repeat  2823    2903    .       +       .       Name=LTR/unknown;family=TE_00001651_INT

chr1    .       Repeat  4411    4473    .       +       .       Name=LTR/Gypsy;family=TE_00002776_INT

I use gt gff3 -sortlines -tidy -retainids cultivar_Lee.repeat.gff3 > cultivar_Lee.repeat.sorted.gff3 to sort my gff3 file, but it delete some lines, why?

   428925 cultivar_Lee.repeat.sorted.gff3

  1194664 cultivar_Lee.repeat.gff3

About half of lines has been delete. My gff file was create by myself use R. I want use tabix for my file. Thank you!

Answer 1

[Philipp Bayer]

I think you changed some more, because 'Family=' is an illegal uppercase attribute, while in your output there's 'family='

There's a good chance that gt gff3 -tidy removes entries with identical IDs/Names/families, and you have Name=LTR/Gypsy;family=TE_00002776_INT many times. One solution is to add your own unique IDs per row.

A workaround is to use standard Linux sort instead:

sort -k 1,1 -k 4,4n cultivar_Lee.repeat.gff3 > cultivar_Lee.repeat.sorted.gff3

[153348734]

Thank your help, I try it, it's useful to me!

Answer 2

[Juke34]

You might find useful information here https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html