jcvi.graphics.karyotype seqids layout: IDs can not found in bed files

[247nahid]

When running:
python -m jcvi.graphics.karyotype seqids layout --figsize 25x25 --dpi 600

I get returned:

OPUNC01G00010 OPUNC01G14970 LOC4326813 LOC4326028 can not found in bed files.

This is just one, what i can see is the entire simple anchor file block list is showing up and is said to not be in the bed files when they clearly are there.

Thanks for any suggestions!

Edit: I shall add that the karyotpye is for a number of genomes (upto 13 at the same time) and the error is for one of the pairwise synteny only. Furthermore, when doing that pairwise karyotype independently the karyotype generation with the same bed and simple.anchor files shows no error.

[tanghaibao]

@247nahid

In the simple anchor file, it should be tab separated. It looks like the four gene (which should be separated by tab) is treated as a single gene and jcvi can't find this in the BED file. Maybe change the space to tab?

[Adamtaranto]

@tanghaibao if there is a central function that imports the blocks/bed/layout files that is used across karyotype and synteny module (I haven't checked) I can add some additional formatting checks for things like this.

[tanghaibao]

@Adamtaranto

Thanks. There are parsers for these formats but there was no validation or checking - which is indeed a problem for ppl working with malformed files.

[Adamtaranto]

Ok I'll try to take a look in the near future.

Things that I recall seeing issues about:

• Spaces instead of tabs
• blank lines
• Additional Hash comment lines
• Windows line endings
• missing / wrong number of columns
• col count does not match track count in layout

Does this just apply to the karyotype, synteny, and ribbon modules?