Changelogs » Alv

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Alv

1.5.0

* New option: `-d` or `--dotted`: the first sequence in the output alignment is used as a template and for positions
  in subsequent sequences that are identical, a period ('.') is output instead of a symbol.
  * Adjustment: replacing blue with cyan in the DNA coloring scheme.

1.4.0

* New option: `-r k` or `--random-accessions k` for only showing a sample of _k_ sequences.
  * New option: `-g` or `--glimpse`: display an informative cut-out of the input MSA, if it does
  not fit without scrolling or line-breaking.

1.3.4

* For some reason, setup.py was/is not putting proper Markdown to PyPi. Solved it halfway. Weird issue.

1.3.3

* Removed bug in alignmnent-type guessing: An MSA without any full codon would be guessed to be
  coding sequences.

1.3.2

* Ensured that alignment text color is black when starting. Helps for those other color preferences
  in the terminal.

1.3.1

* Adding self-promoting --cite and --methods options, noting that there is now a paper
  about `alv` in J Open Source Software.

1.3

* Tick marks come out as ^ on non-UTF systems, instead of an up-arrow on UTF systems (decided by looking at $LANG).
  * Support for Nexus files added (thanks SimonGreenhill)
  * Added CONTRIBUTING.md, a text on how to help develop `alv`.
  * Better README

1.2.0

* The option `-l` colors the alignment but does not break it into blocks. Suitable for piping to `less -RS`,
  as suggested by Mark McMullan <Mark.McMullanearlham.ac.uk>.
  * More indices indicated below alignments, and with an up-arrow as a tick mark.
  * Added option `-sm` to allow restricting output to sequences with accessions containing a given string.

1.1.0

* Implemented format guessing. By default, `alv` tries to identify the alignment format. You can still override if there are parsing problems.
  * You can specify what part of accessions to view with -as. This way you can avoid common prefixes and easily shorten long accessions.
  * View only the first and last N characters of accessions with option -aa.
  * Read from stdin with the magic file name "-".

1.0.5

* Explicitly start with "/usr/bin/env python3" instead of "/usr/bin/env python". Hoping that will
  help users that have not yet migrated to v3.
  * Added v3 requirement in setup.py as well, using advice from Tobias Jakobi. Solves issue 1 on github.com.