sanger-pathogens / pymummer Goto Github PK

View Code? Open in Web Editor NEW

26.0 14.0 11.0 84 KB

Python3 module for running MUMmer and reading the output

License: Other

Python 97.44% Shell 2.56%

pymummer's Introduction

pymummer

Python3 wrapper for running MUMmer and parsing the output.

Introduction
Installation
Usage (for developers)
License
Feedback/Issues

Introduction

Runs MUMmer and parses the output.

Installation

pymummer has the following dependencies:

Required dependencies

MUMmer

There are a number of ways to install pymummer and details are provided below. If you encounter an issue when installing pymummer please contact your local system administrator. If you encounter a bug please log it here or email us at [email protected].

Homebrew/LinuxBrew

brew tap homebrew/python
brew install pymummer

Using pip

pip3 install pymummer

Running the tests

The test can be run from the top level directory:

python setup.py test

Usage (for developers)

Example showing how pymummer can be used to run nucmer on a fasta file and parse the output file to produce a set of alignment objects:

from pymummer import coords_file, alignment, nucmer
...
runner = nucmer.Runner(reference_file, query_file, results_file) 
runner.run()
file_reader = coords_file.reader(results_file)
alignments = [coord for coord in file_reader if not coord.is_self_hit()] #Remove self hits
...

pymummer nucmer class

Wraps the nucmer, delta-filter, show-coords and show-snps commands.

Arguments:

__ref__			reference file  
__query__			query file  
__outfile__		output file  
__min\_id__		min\_id for delta-filter command (default None)  
__min\_length__	min\_length for delta-filter command (default None)  
__breaklen__		breaklen for nucmer command (nucmer's default is 200)   
__coords\_header__	print header in show-coords output (default True)  
__maxmatch__		maxmatch for nucmer (default False)  
__show\_snps__		run show-snps (default False)  
__snps\_header__ 	print header in show-snps output (default True)

pymummer coords_file class

Parses the nucmer output and populate an alignment object for each hit in the output

pymummer alignment class

Check attributes of a hit, swap the reference and query, check if it's a self hit and so on

License

pymummer is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues to the issues page or email [email protected].

pymummer's People

Contributors

Stargazers

Watchers

Forkers

martinghunt nds bede adamtaranto eternal-bug wangpanqiao shafferpr nagesh4193 pathogen-informatics wook2014 rpetit3

pymummer's Issues

MUMmer programs not found in path

Hi , I have no clue why did the installation of pymummer failed even the following programs are in the right folder. I typed "sudo pip3 install pymummer" and I keep getting this error message

nucmer -> /home/ec2-user/software/MUMmer3.23/nucmer
delta-filter -> /home/ec2-user/software/MUMmer3.23/delta-filter
show-coords -> /home/ec2-user/software/MUMmer3.23/show-coords
show-snps -> /home/ec2-user/software/MUMmer3.23/show-snps

Error message.
Complete output from command python setup.py egg_info:
Checking MUMmer programs found in path:
NOT FOUND nucmer
NOT FOUND show-coords
NOT FOUND show-snps
NOT FOUND delta-filter
Cannot install because some programs from the MUMer package not found.

Python 3 pip installation failing

I have tried running installation with python3.6, 3.7, and 3.8 and I get a similar error message with each:

$ python3.6 -m pip install pymummer
Collecting pymummer
  Cache entry deserialization failed, entry ignored
  Cache entry deserialization failed, entry ignored
  Downloading https://files.pythonhosted.org/packages/9f/a4/78890f48a84be3d4733262327da70220be8e11147c7d58b87ea979a0f866/pymummer-0.11.0.tar.gz
    Complete output from command python setup.py egg_info:
    Checking MUMmer programs found in path:
       NOT FOUND        nucmer
       NOT FOUND        show-coords
       NOT FOUND        show-snps
       NOT FOUND        delta-filter
    Cannot install because some programs from the MUMer package not found.
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-ha4k5x9b/pymummer

Is there a fix for this available?

install failure,what should i do?

Collecting pymummer
Using cached pymummer-0.11.0.tar.gz (8.2 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [6 lines of output]
Cannot install because some programs from the MUMer package not found.
Checking MUMmer programs found in path:
NOT FOUND nucmer
NOT FOUND show-coords
NOT FOUND show-snps
NOT FOUND delta-filter
[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.

docs clarification: (1) support for mummer4 (2) support for promer

@martinghunt Could you please clarify two points:

(1) Does pymummer support mummer4?
(2) Does it support promer in addition to nucmer?

Thanks!

What does the "[IDENTITY]" tag means ?

Hi,
In the output of pymummer/nucmer, I got an "IDENTITY" tag in the last column that I don't get with nucmer. What is it's meaning ?

Not related but I also wondered, if it is necessary to calculate an ANI to do it pairwise or if one round is sufficient.

Thank you very much for your answers