search

bioperl / bioperl-live-redmine

Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
0 stars 0 forks source link

PAML parse_PairwiseCodon doesn't parse the ML results correctly #136

Open cjfields opened 9 years ago

cjfields commented 9 years ago

Author Name: Daisie Huang (@daisieh) Original Redmine Issue: 3366, https://redmine.open-bio.org/issues/3366 Original Date: 2012-06-15 Original Assignee: Bioperl Guts

There are spaces present in the output of my PAML (paml4.5) codeml that cause the parsing function to miss the output. I rewrote the regexp piecewise to help make it easier to track these sorts of changes down.

Fundamentally, my PAML puts a space after “dN” and “dS” but before the “=” sign, which makes the regexp not catch them. My patch adds that (“dN\s*\=”) but also breaks the regexp down a bit so that it is easier to understand.

cjfields commented 9 years ago

Original Redmine Comment Author Name: Jason Stajich Original Date: 2012-06-18T09:40:50Z

Thanks Daisie - one thing to speed the time of inclusion of your patch is in the future if you can use github and pull requests to make your patch available directly.

https://help.github.com/articles/using-pull-requests

Hopefully someone can take a look at this in the near term so we can get the changes included.

cjfields commented 9 years ago

Original Redmine Comment Author Name: Daisie Huang Original Date: 2012-06-18T19:03:01Z

Here is a test script that should run correctly after the patch.

cjfields commented 9 years ago

Original Redmine Comment Author Name: Daisie Huang Original Date: 2012-06-18T19:14:03Z

I set up a pull request on github as well, but the comment there (from leto) said that I should include some test files, so I’ve included them here. Is that correct? I am not completely sure how I’m supposed to correlate my github pull request with the bug report; the wiki seems to be out of date on the subject.