phispy - AutoPhispyPIP

This release should automatically create a pip release!

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Published by linsalrob about 4 years ago

phispy - PhiSpy with Colour

A minor bump that removes an edge-case error in the colour definition testing

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Published by linsalrob about 4 years ago

phispy - Dropped prophages

This release adds an option to retain dropped putative prophage regions in the GFF3/GenBank files so you can explore them manually e.g. in artemis

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Published by linsalrob over 4 years ago

phispy - v4.2.15 great gff3

We have added gff3 support to write the whole genome, including the annotated prophage regions.

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Published by linsalrob almost 5 years ago

phispy - v4.2.12 tidying up

Most of the changes in the new version are minor changes that all add up to cleaner code and better results

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Published by linsalrob almost 5 years ago

phispy - ValueError Free Release

Fixing the ValueError error that plagues biopython

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Published by linsalrob over 5 years ago

phispy - Version 4.1.20 Improved metrics parsing

Resolved parsing the --metrics options, so you can either add one --metrics flag and list all your options, e.g.

PhiSpy.py --metrics shannon_slope gc_skew

or provide each one with its own flad, e.g.:

PhiSpy.py --metrics shannon_slope --metrics gc_skew

This is a combination of using argparse append and then iterating the list.

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Published by linsalrob over 5 years ago

phispy - Version 4.1.18 improved metrics parsing

The version solves an issue with parsing the metrics from the command line.

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Published by linsalrob over 5 years ago

phispy - Version 4.1.16 many enhancements

Lots of enhancements and tweaks since the last release. This version is also available in PyPi and Conda.

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Published by linsalrob over 5 years ago

phispy - Version 4.0.0

This is version 4.0.0 of PhiSpy. A new release with a whole raft of changes and improvements, bug fixes, and speed up.

You should update to version 4.0.0. using pip install --upgrade phispy or conda update phispy as appropriate. See the Installation Instructions.

See the README for more details about the improvements and enhancements

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Published by linsalrob almost 6 years ago

phispy - Version 4.0.0 release candidate 1

This is the first release candidate of version 4 that includes a suite of new features and outputs.

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Published by linsalrob almost 6 years ago

phispy - pip and conda versions

A version that is acceptable to PyPi and bioconda for easy installation.

PyPi allows easy installation with pip. See the PhiSpy project page.

bioconda allows easy installation with conda. See the PR to integrate PhiSpy with bioconda.

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Published by linsalrob about 6 years ago

phispy - Improvements to repeatfinder

In this release we internalize repeatfinder to become a python external module that we have renamed PhiSpyRepeatFinder as there are many other modules called RepeatFinder out there. The C++ code is now directly called from the Python code, removing the need for some confusing temporary files.

We have also initiated the availability of PhiSpy through PyPi by adding setup.py.

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Published by linsalrob about 6 years ago

phispy - Version 3.4.5

Several important fixes and improvements following our v3.4 release and we are on the way to v3.5, but wanted to get these out sooner.

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Published by linsalrob over 6 years ago

phispy - Version 3.4

We have made many updates and changes between v3.3 and v3.4 and most of that work has been done by @deprekate and @pdec.

We have fixed numerous issues, moved away from R to keep the random forests in Python, redeveloped the k-mers, and many, many other changes.

If you find issues with version 3.4, please post them under issues.

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Published by linsalrob over 6 years ago

phispy - Version 3.4 prerelease

This is version 3.4 prerelease for testing. Please create an issue if you find one.

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Published by linsalrob over 6 years ago