bioperl/bioperl-run

Add Amap, Kalign and Probcon Quiet option

cjfields opened this issue · 2 comments

cjfields commented

Author Name: Nathan S. (Nathan S.)
Original Redmine Issue: 2127, https://redmine.open-bio.org/issues/2127
Original Date: 2006-10-26
Original Assignee: Bioperl Guts

Figure out if Amap, Kalign and Probcon can have a quite option to stop output to screen. I know Amap specifically writes output to STDOUT, but this could be redirected to a file and then read back in if required while STDERR is redirected to /dev/null.

cjfields commented

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2007-01-02T14:18:06Z

According to the mail list:

http://bioperl.org/pipermail/bioperl-l/2007-January/024554.html

Sendu is planning on adding a quiet() method for anything implementing WrapperBase. Would that help?

cjfields commented

Original Redmine Comment
Author Name: Nathan Haigh
Original Date: 2007-01-02T15:33:11Z

It may well help. However, if I remember correctly, I think some actual data is printed to STDOUT…..although this might be meta-data for eye-balling/interpreting results manually - I’m not familiar with these programs. Hopefully, the tests will catch anything that breaks!