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Hi, is there any option to flip specific chromosomes of specific species to untangle the ribbon plot?

victor4110

Error in rule plot_synteny_nocolor

1

As the title says, I'm getting an error in rule plot_synteny_nocolor with the following config: ``` ignore_autobreaks: True # Skip steps to find breaks in synteny blocks diamond_or_blastp: "diamond" #...

HX-FAshur

This has the potential to be misinterpreted due to I, II, III. Instead, give an example genome assembly file. ``` # this file is called config.yaml ignore_autobreaks: True # Skip...

conchoecia

segmentation fault following Matplotlib GUI usage warning - QObject::killTimer: Timers cannot be stopped from another thread

1

I am using the script for running the odp_basic test case, and I am receiving a segmentation fault following Matplotlib GUI usage warning, similar to the issue https://github.com/conchoecia/odp/issues/61. The exceptions...

AdamVS

example input files

1

Dear conchoecia, Thank you for preparing this useful script, may I ask where could find the example input files for reproidcuing the Ribbon Diagrams you presented in the manual page?...

songweizhi

config file for ALGs part 7 - Plot mixing of select linkage groups

1

Hello, I can not find the config file for ALGs part 7 - Plot mixing of select linkage groups. Did I miss something? Thank you very much for your help...

Taojianchang

See this issue: https://github.com/conchoecia/odp/issues/50 TODO - implement a .chrom parser that checks that the number of columns is correct, and that the data type in each column is correct.

conchoecia

NCBIgff2chrom -> gxf2chrom

2

Hi @conchoecia! I developed this: [gxf2chrom](https://github.com/alejandrogzi/gxf2chrom), while thinking about your NCBIgff2chrom.py script! In short, this is a CLI-tool written in Rust that does basically the same exact thing your script...

alejandrogzi

IndexError: list index out of range

2

Could someone please help with the error? snakemake --snakefile /home/snp/odp/scripts/odp -c1 Building DAG of jobs... InputFunctionException in rule hmm_1_against_prots in file /home/snp/odp/scripts/odp, line 2133: Error: IndexError: list index out of...

sim3023

find duplicate protein substrings with cd-hit

2

use cd-hit to find duplicate protein substrings in the input protein files use this for "best" filtering option needs these files: cd-hit cdhit.c++ cdhit-common.h cdhit-common.o cdhit.o cdhit-utility.o Makefile license.txt

conchoecia