nibtehaz / ssg-lugia

Hi there 👋, my No. vistor!

About Me

• I'm currently a CS PhD Student at Purdue University.
• I received my BSc (EEE) and MSc (CSE) degree from Bangladesh University of Engineering and Technology.
• My interests include Computer Vision, Biomedical Image and Signal Processing, Bioinformatics
• Feel free to contact me: [email protected]

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ssg-lugia's Issues

SSG_LUGIA works with Fragmented Genomes?

Hello again!

I have tried to run SSG_LUGIA with fragmented genomes and it gives me the following error.

SSG_LUGIA('/xxxxxx/Software/SSG-LUGIA/codes/sample_data/genome_fragmented.fasta', model_name='SSG-LUGIA-F')
Traceback (most recent call last):
File "", line 1, in
File "/datos1/xxxxx/Software/SSG-LUGIA/codes/main.py", line 30, in SSG_LUGIA
genome = loadGenome(sequence_fasta_file_path)
File "/datos1/xxxxx/Software/SSG-LUGIA/codes/file_handling.py", line 18, in loadGenome
genome = SeqIO.read(file_path,'fasta')
File "/home/xxxxx/anaconda3/lib/python3.7/site-packages/Bio/SeqIO/init.py", line 754, in read
raise ValueError("More than one record found in handle")
ValueError: More than one record found in handle

With complete genomes it works perfectly, I imagine that the fragmented ones don't work but anyway I wanted to ask

Thanks for your time and patience!

Problems running SSG_LUGIA

Hello! Thank you for your software and for the time it took you to answer this.
Try to download from the repository and after installing the requirements I activate Python3 and use

from main import SSG_LUGIA

and enter the command

SSG_LUGIA('/My_sequence_path/='file.fasta' ,model_name='SSG_LUGIA-F')
File "", line 1
SSG_LUGIA('/My_sequence_path/='file.fasta' ,model_name='SSG_LUGIA-F')
^
SyntaxError: invalid syntax

I don't know much about programming, I'm trying to learn and I would appreciate your help infinitely

Annotation file

Hello

How can I provide an annotation file in addition to the non-annotated file? In that case, which file would work?

Greetings