Menu

#365 BLAT plugin feature enhancements and bug fixes

v2.0
open
Gbrowse (196)
5
2011-04-29
2011-04-29
No

I have implemented a few bug fixes and functionality enhancements to the
GBrowse 2.26 BLAT plugin that would likely appeal to other users of the
plugin.

Changes:

* Allow the user to enter an optional FASTA defline (frequently users
would include a defline & wonder why nothing was being returned).
This fixes this previously-reported issue:

https://sourceforge.net/tracker/index.php?func=detail&aid=2927805&group_id=27707&atid=391291

* Return a "No alignments found" message if none were found. The current place
this is displayed -- the "Landmark or Region box -- isn't ideal, but it's
less confusing than not returning any message.

* If an amino acid sequence contained one of [ACTGN], check_seq() would assume
it's DNA; this updated version checks considers the sequence to be an amino
acid sequence if it has a non-[ACTGN] amino acid, else it's considered to be
DNA.

* Append a number to the name of each created "Alignment" feature so it is
unique; this way, the links in the "Name" column of the multiple hits page
work (previously, clicking on any "Alignment" link in the "Name" column
always linked to the first Alignment listed).

* Removed references to "human" and "mouse" from the description.

* capture the stderr of the gfClient command and display it if there is any.

* (optimization) Stop processing results after the first $hits alignments.

PREREQUISITES:

Finder plugins don't work in the default gbrowse 2 when invoked from the
browser due to a JavaScript issues reported here:

https://sourceforge.net/tracker/index.php?func=detail&aid=3141696&group_id=27707&atid=391291

I had patched my htdocs/js/controller.js using the method I reported in the
comment.

Discussion

  • Nathan Weeks

    Nathan Weeks - 2011-04-29
     
  • Scott Cain

    Scott Cain - 2011-04-29
    • assigned_to: scottcain --> lstein
     

Log in to post a comment.

MongoDB Logo MongoDB