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possible error in and fix

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possible error in and fix

Dear fellows,

thank you for the newly rewritten version of in Rosetta 3.4 ... it came just in time when I was struggling with the old one! In my hands/case though, there was a problem with the inclusion of secondary structure prediction from pre-calculated files. (It worked well when files were calculated on the fly with psipred / SAM installed.)

I'll try to be exact with my description of the errors in the current version:
1) Filenames like "test1_psipred.ss2" when given with -psipredfile are read into $options{psipredfile}, but in the subroutine file_overrides_option is called with $options{psipred_file}. Therefore, in its current version always tries to run psipred (or SAM/porter).

2) Inclusion of the secondary structure predictions in the flags handed to picker and in the score.cfg and quota.def files are governed by the $options{psipred/sam/porter}, which is 0 if the programs are not run, but only the .ss2 file is included with the according option, like -psipredfile *.ss2. Therefore, only if tries to run psipred/SAM/porter the results are included in the scoring.

I came up with a fix for both making minimal changes to which I tested and which worked in my hands. A diff output file shows only the changes I made. Both files are attached as text files.
I'd be happy about a further comment and hope everything works nicely now :)


Post Situation: 
Fri, 2012-04-27 02:23

posting here with file uploading & preview didn't work...
Could somebody delete the other "spam" posts.. sorry!

I'll try to attach the diff file here.


Fri, 2012-04-27 02:32

...and the script :)

Fri, 2012-04-27 02:33