MSAViewer

Description
This extension provides a simple file formatter for genomic sequence alignements files and a text filter using the library MSAViewer¹ for display.


1: Yachdav, Guy, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna E. Lewis, Burkhard Rost, and Tatyana Goldberg. "MSAViewer: interactive JavaScript visualization of multiple sequence alignments." Bioinformatics (2016): btw474.


Installation

• Install as you would normally install a contributed Drupal module. See:
  https://drupal.org/documentation/install/modules-themes/modules-7
  for further information.
• Install the MSAViewer library:
  download https://cdn.bio.sh/msa/1.0/msa.min.gz.js
  and save it to a msaviewer directory in your library directory (so
  you should have: .../sites/XXX/libraries/msaviewer/msa.min.gz.js).
  Then unzip it to have an "msa.js" file:
  gunzip msa.min.gz.js -c > msa.js
• Enable the module in "Admin menu > Site building > Modules" (path
  /admin/modules).

Use
Example 1:

• Create or use an existing content type.
• Add a "file" field to that content type (admin/structure/types --> manage fields).
• Change the formatter of that file (manage display) to use "MSAViewer".
• Create a corresponding content with an alignment file (FASTA, Clustal,...) and display it.

note: this formatter can also be used in views or other places and it supports
multiple trees on a same page.


Example 2:

• Edit a text format (admin/config/content/formats) and check the filter "MSAViewer Filter".
• In the "Filter processing order" section, make sure the filter "MSAViewer Filter" comes before other filters which may alter HTML tags and save.
• Create a new content that has a (multiple lines) text field.
• Add a tag <msaviewer url="[URL to an alignment file]"> in the text field.
• Select the text format that uses the "MSAViewer" filter and save.