GenGraph

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Hello, I'm a students trying to create a graph similar to figure 3 of the GenGraph paper. I've been trying to get the code to run for more that a...

eros273

No such file or directory: 'globalAlignment_khush.backbone'

10

Hey, I am trying to run example code in your repo(sequences.txt) with some modifications in local system but I am having this problem. ``` $ python3 ./gengraphTool.py make_genome_graph --seq_file sequences.txt...

Logan1x

The current release still shows 'Welcome to GenGraph v0.1' in the help even though the Git release is tagged as 0.3.

russellsmithies

Hi! i am quite new in this field and i struggle to understand the difference between vg and this library, can you help me? Thank you in advance and thank...

minu7

[HELP / FEATURE] is it possible to use a single fasta file containing many genomes?

1

The national library of medicine (https://www.ncbi.nlm.nih.gov/datasets) only allows you to download a list of genomes in a single fasta file (extension .fna), I tried to provide those files as input...

minu7

Gengraph running problem

28

hi One question Why when I start running the program (base) devina@Devinas-MacBook-Pro ~ % python3 GenGraph/gengraphTool.py make_genome_graph --seq_file Documents/anagengraph.txt --out_file_name Documents/output Conducting progressiveMauve progressiveMauve It got stuck. I am using...

Devinaseeruttun

set mauve scratch path

21

--scratch-path-1 is hard-coded. This needs to become relative.

jambler24

TypeError: set_node_atttributes() missing 1 required positional gengraph argument: 'values'

2

 Haven't made any change to the original scripts. Still facing this issue

jainv45

Look into using PyPy

3

It is possible that this tools can benefit from the JIT compiler.

jambler24

Create a function to convert to and from gfa format used by vg. The format is defined here: https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md This may be tricky as at first glance vg does not...

jambler24