odp

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problem converting gff

3

Hi, I am trying to convert a gff to a .chrom. The script works with the example python NCBIgff2chrom.py GCF_000001405.39_GRCh38.p13_genomic.gff.gz > GCF_000001405.39_GRCh38.p13_genomic.chrom. However, it does not work with the two...

pedres

remove awk dependency

1

there are still some occurrences of awk in genome_rearrangement_simulation

conchoecia

remove dependency on seaborn

3

conchoecia

Sometimes, the interval for the proteins in the genome are incorrect. For example, in this example for the Hydra genome available on NCBI: ``` protein scaf strand start stop length...

conchoecia

Hi Darrin, I have noticed that, on multicore systems, the default `Makefile` doesn't have a `--cores` flag, which causes compilation to fail. This small change fixed it for me. I...

xgrau

docker image

1

I am having too many issues working around all the dependencies versions in order to install odp. Is there any docker image that I can import. Thanks very much

phbrito

Haven't been able to test. Changed two files to add options for repeating sequential color palettes instead of random.

beroe

make odp_nway_rbh plot a ribbon diagram

8

The species order can be set by specifying the order in the analyses section.

conchoecia

There is an error where, when the ribbon diagram pdfs are opened in Adobe Illustrator, that each line is surrounded by a clipping mask. This inflates that object count in...

conchoecia

Sometimes manuscripts define LGs to be based on the genes of one species, like the CLGs in [Simakov et al 2020](https://www.nature.com/articles/s41559-020-1156-z). The ALG database functionality needs to be changed to...

conchoecia