millstone | Genome engineering and analysis software | Genomics library

by churchlab Python Version: 1.0 License: MIT

X-Ray Key Features Code Snippets(3)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | millstone Summary

millstone is a Python library typically used in Artificial Intelligence, Genomics applications. millstone has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However millstone build file is not available. You can download it from GitHub.

Millstone is a distributed bioinformatics software platform designed to facilitate genome engineering for synthetic biology. Automate iterative design, analysis, and debugging for projects involving hundreds of microbial genomes.

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Quality

Security

License

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Support

millstone has a low active ecosystem.

It has 47 star(s) with 18 fork(s). There are 14 watchers for this library.

It had no major release in the last 12 months.

There are 156 open issues and 472 have been closed. On average issues are closed in 542 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of millstone is 1.0

Quality

millstone has no bugs reported.

Security

millstone has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

millstone is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

millstone releases are available to install and integrate.

millstone has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed millstone and discovered the below as its top functions. This is intended to give you an instant insight into millstone implemented functionality, and help decide if they suit your requirements.

Retrieve callable Lociations from BAM file
Exports a list of contigs to a VCF file
Returns the next letter
Gets the absolute path of the file
Given a list of reference_genome_genome_genome
Generate a safe filename prefix from a label
Removes whitespace from a string
Create a bam file for de novo alignment
Get unmapped reads from samtools
Get reads in interval list
Create a linkage field for the given variant row
Creates the sqlite3 database
Exports a Melted variant
Create alt flag field for a variant
Add BAM track for a contig
Adds reads to the BAM track
Run Delly
Adapters to frontend
Run pindel
Creates a frontend document from a list of experiments
Generates a list of maigos for a given variant set
Minimal bwa alignment
List a single variant set
Looks up the genes in the alignment group
Combine a pindel VCF file into a single VCF
Render a project root

Get all kandi verified functions for this library.

millstone Key Features

No Key Features are available at this moment for millstone.

millstone Examples and Code Snippets

Developer Documentations,Tests

Python

Lines of Code : 8

License : Permissive (MIT)

Copy

(venv)$ ./scripts/run_unit_tests.sh

(venv)$ ./scripts/run_integration_tests.sh

(venv)$ ./scripts/run_unit_tests.sh main

(venv)$ ./manage.py test --settings=tests.integration_test_settings tests/integration/test_pipeline_integration.py:TestAlignmen

Developer Documentations,Tests,Debugging Tests / Dealing with Craziness

Python

Lines of Code : 6

License : Permissive (MIT)

Copy

AssertionError: No running Celery workers were found.

ps aux | grep celery

ps aux | grep python.*integration

kill 777

./scripts/kill_celerytestworkers.sh

./manage.py test -s --settings=tests.integration_test_settings tests/integration/test_pipel

Developer Documentations,Debugging,Logging

Python

Lines of Code : 3

License : Permissive (MIT)

Copy

    import logging
    LOGGER = logging.getLogger('debug_logger')

    LOGGER.debug('string or variable you want to log')

Community Discussions

Trending Discussions on millstone

Replace substrings with object property using flag character

QUESTION

Replace substrings with object property using flag character

Asked 2018-Apr-25 at 20:23

I need to replace generic substrings marked with a flag character with specific values from a custom object. I have written the code that accomplishes what I want, though it feels awkward. I'm wondering if there is a more sophisticated solution to this issue. Specifically, I'm wondering if there is a quick function to replace so-marked substrings with other values, dependent on the generically occurring substring.

Here's my current code:

...

ANSWER

Answered 2018-Apr-25 at 20:23

You could use a regular expression to pull out all of the tokens and use Replace() to substitute in the values.

Source https://stackoverflow.com/questions/43874646

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install millstone

These are directions for installing Millstone on your own machine, and is meant for advanced users who want a custom installation. If you want to deploy a pre-configured Millstone instance to the cloud, then read Getting Started with Millstone on the wiki.