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I am trying to install by using this code pip install Magphi and I got this error
Collecting Magphi
Downloading Magphi-2.0.0-py3-none-any.whl (29 kB)
Requirement already satisfied: biopython==1.79 in ./miniconda3/lib/python3.9/site-packages (from Magphi) (1.79)
Collecting pybedtools
Downloading pybedtools-0.9.0.tar.gz (12.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.5/12.5 MB 38.9 MB/s eta 0:00:00
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [30 lines of output]
Traceback (most recent call last):
File "", line 2, in
File "", line 34, in
File "/private/var/folders/_t/bn8_sf0977n5x0zjh0xsf2xr0000gn/T/pip-install-i652sgvi/pybedtools_ffacbbbf6e474788849b95a2c5852cd2/setup.py", line 286, in
setup(
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/init.py", line 86, in setup
_install_setup_requires(attrs)
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/init.py", line 75, in _install_setup_requires
dist = MinimalDistribution(attrs)
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/init.py", line 57, in init
super().init(filtered)
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/dist.py", line 474, in init
for ep in metadata.entry_points(group='distutils.setup_keywords'):
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 999, in entry_points
return SelectableGroups.load(eps).select(**params)
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 449, in load
ordered = sorted(eps, key=by_group)
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 996, in
eps = itertools.chain.from_iterable(
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/_itertools.py", line 16, in unique_everseen
k = key(element)
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 931, in _normalized_name
return self._name_from_stem(stem) or super()._normalized_name
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 600, in normalized_name
return Prepared.normalize(self.name)
File "/Users/mo/miniconda3/lib/python3.9/site-packages/setuptools/vendor/importlib_metadata/init.py", line 855, in normalize
return re.sub(r"[-.]+", "-", name).lower().replace('-', '')
File "/Users/mo/miniconda3/lib/python3.9/re.py", line 210, in sub
return _compile(pattern, flags).sub(repl, string, count)
TypeError: expected string or bytes-like object
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

I tried also conda and it failed

Review

I am not sure if the tests have actually failed or the tag in the GitHub readme has just failed to update. In either case, it would be good to re-run the tests so that the tag updates to green.

Add in a flag or two that will indicate if a single/all input genomes are complete and circular, or a flag that can take a text file with each genome in it and a matching indication if it should be treated as circular.

script appears to fail when two primer sets are named similarly enough to fail one of the functional checks (for example D_1/2 and mutsD1/2) this appears to be fixed when having a longer primer sequence name to prevent non uniqueness in names (ie. adding site to the beginning of everything fixed it.

python3 primer_site_extraction_software-main/main.py -g /Users/ahhayes/Desktop/lab-book/100_YR_M1/genomes/091219-final-fasta/*.fa -p Javan_phage_int_sites_M1_no_g.fa -o MGAS5005_Javan_all -c 4
all files were found to be fasta files
Trying to construct output folder...
Output folder exists
42 primers found in primer file.
This leads to 21 pairs of primers.
concurrent.futures.process._RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/Users/ahhayes/miniconda3/envs/extractor/lib/python3.6/concurrent/futures/process.py", line 175, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/Users/ahhayes/Desktop/lab-book/Magnus/extractor/primer_site_extraction_software-main/search_insertion_sites.py", line 620, in screen_genome_for_primers
    genome_file, file_type, tmp_folder)
  File "/Users/ahhayes/Desktop/lab-book/Magnus/extractor/primer_site_extraction_software-main/search_insertion_sites.py", line 395, in check_primers_placement
    raise NotImplementedError(f'Some unaccounted for constalation of primers hits '
NotImplementedError: Some unaccounted for constalation of primers hits was found to hit a single contig.
The primer pair in question is D in genome MGAS5005_Javan_all/phupa_tmp_folder/13670_4_14.fa.
Please report this along with the following: [['contig00002', '24993', '26391', 'D_2'], ['contig00002', '26523', '27435', 'D_1'], ['contig00002', '270018', '272574', 'mutsD_2'], ['contig00002', '272702', '274685', 'mutsD_1']]
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "primer_site_extraction_software-main/main.py", line 122, in <module>
    main()
  File "primer_site_extraction_software-main/main.py", line 75, in main
    primer_hits, annots_per_interval, genome_name, primer_evidence, break_primers, inter_primer_dist = f.result()
  File "/Users/ahhayes/miniconda3/envs/extractor/lib/python3.6/concurrent/futures/_base.py", line 425, in result
    return self.__get_result()
  File "/Users/ahhayes/miniconda3/envs/extractor/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
NotImplementedError: Some unaccounted for constalation of primers hits was found to hit a single contig.
The primer pair in question is D in genome MGAS5005_Javan_all/phupa_tmp_folder/13670_4_14.fa.
Please report this along with the following: [['contig00002', '24993', '26391', 'D_2'], ['contig00002', '26523', '27435', 'D_1'], ['contig00002', '270018', '272574', 'mutsD_2'], ['contig00002', '272702', '274685', 'mutsD_1']]

Review

Currently, the dependencies are only listed as part of a conda command. I think JOSS requires that these are given as a separate section in the documentation.

[Review = https://github.com/openjournals/joss-reviews/issues/4369]

• The command for the toy example needs updating. It currently refers to fasta files but there are only GFF files in the Toy_example/Input_data folder.
• I am not sure whether it was intentional to keep the Toy_output folder in the GitHub repository. I think it might be better to simply list the files and folders that should be creates in the documentation
• I think the description of the output of the toy example in the Wiki could be improved. A few sub-headings might also help to make it easier to follow.
• I think this is quite a nice example and if it is formatted a bit more cleanly it would make a nice addition to the main Readme.md file. However, I'll leave this entirely up to you as I think it is okay in its current location also.

Review

The paper is well written, however, there are quite a few typos in the Readme and Wiki. There are GitHub actions to check spelling, but I think it might be easiest to simply copy the .md files into a word editor such as Google docs to help clean up the remaining typos.

A few I've spotted include:

• Readme and wiki: 'Examlpe', 'seqeunces', 'imporive' ...
• Wiki - installation: 'seqeunce', 'Qucik', 'writen', 'Comming', 'recipie', ...

Implement a check that looks for possible annotations related to the coordinates of the primers.
These annotations needs to be taken into account when assigning evidence levels, as a region can contain no annotations in itself, but if the primers are included and contain annotations, the evidence level is increased falsely.

Hey guys, I'll be reviewing this repository and the paper on behalf of JoSS! This is my main review thread, in which I'll discuss things with you guys. If there is a specific issue we need to address, I'll open a separate issue and link it here. Once my review is done, and everything is resolved, I'll close this issue.

Review

It would be good to make Magphi available on bioconda. This is mentioned in the documentation but not yet completed.

In situations where a seed coming from a gene in the reverse orientation is oriented by the GFF is not correct.
Run with -S for now with still works

Review

JOSS requires that there is a community guidelines section in the documentation.

Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Add the possibility of giving the primer pairs as two command line flags.