Skip to content

Latest commit

 

History

History
98 lines (56 loc) · 3.21 KB

CHANGES.md

File metadata and controls

98 lines (56 loc) · 3.21 KB
Raw

Changes since last version

v1.8.0

  • Added support for selecting sub-alignments. See option -sa

v1.7.2

  • Ed Davies fixed a bug: sorting using option -so was broken

v1.7.1

  • What??

v1.7.0

  • Added the option --alignment-index to support files with multiple MSAs.
  • Added two functions, view and glimpse, to enable use of alv in notebook environments.

v1.6.1

  • Fixed accession abbreviation so that short accessions are left as they are.
  • Requiring python 3.5 or later, because Colorama has droppen support for 3.4.

v1.6.0

  • New options: --only-variable and --only-variable-excluding-indels, contributed by nikostr. Constrains coloring to columns with variation and variation not counting indels.
  • Fixed the --dotted option, which only worked with the first block for DNA sequences. Also improved the coloring which was too ugly in dotted mode (due to laziness).

v1.5.0

  • 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.

v1.4.0

  • 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.

v1.3.4

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

v1.3.3

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

v1.3.2

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

v1.3.1

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

v1.3

  • 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

v1.2.0

  • The option -l colors the alignment but does not break it into blocks. Suitable for piping to less -RS, as suggested by Mark McMullan [email protected].
  • 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.

v1.1.0

  • 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 "-".

Introduced in version 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.