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In terms of getting socru packages in non-conda systems it would be good to know what it depends on.

I am interested in how sequences are rated as being either GREEN, AMBER or RED by Socru.
Can you elucidate the criteria for each of the ratings?

running socru-2.2.2 with PyYAML 5.1 generate a warning

see:

c6builder:socru/2.2.2 > socru Escherichia_coli ../../datas/socru/ecoli.fa
/local/gensoft2/exe/socru/2.2.2/lib/python3.6/site-packages/socru/Profiles.py:39: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  metadata = yaml.load(metadatafh)
../../datas/socru/ecoli.fa      GREEN   GS1.0   1       2       3       4      56       7

easy fix is to change yaml.load(call) in Profiles.py
from

metadata = yaml.load(metadatafh)

to

metadata = yaml.load(metadatafh, yaml.SafeLoader)

regards

Eric

Getting this error when running socru_species:

Schemas().print_all()
TypeError: __init__() missing 1 required positional argument: 'verbose'

I installed socru using conda, and socru by itself seems to work fine (or print out the help message at least). I checked that I have python 3.7 installed.

I ran Socru version 2.2.4 and got the file described as 'Pimary output' in the documentation. The pirmary output contained the expected number of lines compared to the number of genomes given as input. However, I did not get any other output files.

The command I ran was:
socru Streptococcus_pyogenes File/Path/to/*.fna -t 16 --output_file File/Path/to/Refseq_Socru_140520 -v

I looked in the verbose output for clues to the missing output files but could not identify any.
I would expect to get other outputs like the operon_directions.txt, but why are they not given?
Thank you in advance!

Describe the bug
I have a problem running Socru on Campylobacter jejuni assemblies. The Campylobacter genome can be separated into three fragments separated by ribosomal operons. For Campylobacter coli, the origin of replication (Ori) is in fragment 3 and the terminus (ter) is in fragment 1, and Socru can easily be used to identify misassembles for this species. However, for Campylobacter jejuni Ori and Ter are both on fragment 1. Because of this, Socru always calls the assemblies invalid.

Campylobacter jejuni RED GS1.0 1 2 3 Invalid --> 1(Ori)(Ter) --> 2 --> 3
Campylobacter coli GREEN GS1.0 1 2 3 Valid --> 1(Ter) <-- 2 <-- 3(Ori)

In addition, the operon direction file always shows Ori and Ter in alphabetical order on fragment 1, making it difficult to determine if the assembly is valid using Socru. To test this I took a C. jejuni chromosome, determined its reverse compliment and placed it through Socru, and Ori was still before Ter on fragment 1.

Normal Campylobacter jejuni RED GS1.0 1 2 3 Invalid --> 1(Ori)(Ter) --> 2 --> 3
Reverse compliment Campylobacter jejuni RED GS1.0 1 2 3 Invalid <-- 1(Ori)(Ter) <-- 3 <-- 2

Therefore, if Ori and Ter are on the same fragment can Socru be changed to give the order of Ori and Ter as they appear on the fragment, and can it call C. jejuni assemblies with Ori and Ter on fragment 1 valid.

Have been using Socru previously but had to reinstall and when using the conda installation I got the following error:

Traceback (most recent call last):
  File "/home/georgia/miniconda3/envs/python3.6/bin/socru", line 10, in <module>
    from socru.Socru import Socru
ModuleNotFoundError: No module named 'socru' 

The pip installation worked fine so I'm happily using this but just wanted to alert to the fact that the Conda installation had issues.

For reference the conda install was into a clean environment on a linux machine.

Hi,

First of all, thanks for writing this piece of software, I wonder it I can use it for detecting genome rearrangements mediated by other sequences such as IS elements?

Thanks,
Dorothy

Describe the bug

Hi, I installed socru using Conda v 2.2.4 and got this error when I tried it on an isolate

Traceback (most recent call last):
File "/Users/a1667917/mambaforge/envs/socru/bin/socru", line 10, in
from socru.Socru import Socru
File "/Users/a1667917/mambaforge/envs/socru/lib/python3.9/site-packages/socru/Socru.py", line 13, in
from socru.FragmentFiles import FragmentFiles
File "/Users/a1667917/mambaforge/envs/socru/lib/python3.9/site-packages/socru/FragmentFiles.py", line 4, in
from Bio.Alphabet import generic_dna
File "/Users/a1667917/mambaforge/envs/socru/lib/python3.9/site-packages/Bio/Alphabet/init.py", line 20, in
raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

Additional context
This error was fixed when I commented out socru/FragmentFiles.py line 4 and socru ran fine without any issues.

George