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symgenoevolab / SyntenyFinder

SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.
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Dependencies directory missing? #1

Closed sskspider closed 6 months ago

sskspider commented 6 months ago

Hi, this looks like a great tool from your preprint, congratulations! I tried to use the code on a Linux machine and have a couple of questions:

  1. the "dependencies" directory (including Synteny_functions.py and Bfl folder) in the main directory (as shown by the directory contents figure in the README.md) is missing. I copied the "dependencies" directory from "Bryozoan_Synteny" folder, but got the error "ModuleNotFoundError: No module named 'dependencies.Synteny_functions'" I have orthofinder, pandas and biopython installed. Am I missing something?
  2. How can I use an unpublished genome (chromosomal and annotated) using this pipeline?

Thank you. Siddharth.

ijyliao commented 6 months ago

Dear Siddharth,

Thank you for your interest in our work! Apologies for the inconvenience; since our work is still a preprint, some of the genome data is not yet available and I had missed uploading the dependencies folder in the confusion. The directory should now be available. Some of the Bfl files, namely Bfl_gene_rows.gtf and Bfl.fna are not available from our repository but can be downloaded from their original source here. I have reflected these changes in the README but please by all means let me know if you have any additional questions.

The main pipeline is currently only usable with NCBI-available genomes in order to keep the process streamlined and accessible; however, the jupyter lab version within the directory Bryozoan_Synteny is considerably more powerful and can work with multiple formats of genome annotations. The file structure is a little different, but the instructions are directly integrated into Bryozoan_Synteny/Synteny_main.ipynb.

Cheers, Isabel

sskspider commented 6 months ago

Thanks Isabel, it worked!