Software for working with sequence annotations

Question

[massa.kassa.sc3na]

Hi,

I'm looking for a command-line tool / library for working with sequence annotations. It should support following

• import annotations from .gff / .gtf formats (other usual formats are also fine)
• import some very basic data format (like csv) to read user defined data (regions of interest - ROI)
• provide functions for:
  • finding annotations upstream / downstream from ROI,
  • finding annotations within certain range, overlapping ROI
  • allowing to filter the annotations based any criteria (from sequence annotations, mutual distance or overlaps, strand, etc.)
  • allow detection of duplicated entries
  • ability to specify "wiggle" room for the operations
• exporting selected annotations

For now I'm using BioPython + pandas, however I'm wondering if there is a better solution.

Thanks

[GenoMax]

One tool from @Juke-34 that may be of interest : AGAT

[massa.kassa.sc3na]

Thank you, I've skimmed through the documentation and this ticks some of the boxes. I'll probably use it some day.

[Joe]

Its very unlikely you're going to find a single tool that can do all of these things ready made. Off the top of my head, some tools that may be able to address one or more might be:

• Snapgene
• Geneious
• CLC Workbench
• Artemis
• DNAStar

Cloning software is usually pretty good for manipulating annotated sequences. Several of the tools in that list are not free however unfortunately.

[massa.kassa.sc3na]

Thank you for the suggestions, I'll look into them.

[massa.kassa.sc3na]

While searching for something else I've stumbled upon the bedtools programs intersect and closest, which both are something along the lines of what I was looking for. Leaving comment for anybody who might find it useful.

Links:

https://bedtools.readthedocs.io/en/latest/content/tools/closest.html

https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html