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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> inputRedirect syntax http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1193604210 Message started by kai42 on Oct 28^th, 2007 at 1:43pm

Title: inputRedirect syntax
Post by kai42 on Oct 28^th, 2007 at 1:43pm

Hi,

when I try to run the following batch file:

Code (]
inputRedirect={};
inputRedirect["01"):

="Universal";
inputRedirect["02"]="C:\Program Files\HYPHY_Win32\clpP.fas";
inputRedirect["03"]="None";
inputRedirect["04"]="Default";
inputRedirect["05"]="Default";
inputRedirect["06"]="C:\Program Files\HYPHY_Win32\test.tre";
inputRedirect["07"]="Node15";
inputRedirect["08"]="1";
ExecuteAFile("C:\Program Files\HYPHY_Win32\TemplateBatchFiles\TestBranchDNDS.bf", inputRedirect);

.... I get the following error:
[code]
Error:Not a valid (or duplicate) option: '1' passed to Choice List (with multiple selections) 'Choose the branch to test' using redirected stdin input
Current BL Command:Choice List for Choose the branch to test with choice list:NO_SKIP. Store result in bOption[/code]

How can I (can I?) properly put branch/parameter choices in the inputRedirect array?

Thanks a lot in advance for any hints....

Kai

Title: Re: inputRedirect syntax
Post by Sergei on Oct 28^th, 2007 at 2:39pm

Dear Kai,

Try using "" (empty string) as the value of the input string indexed ["08"]; an empty string signals to HyPhy that the multiple selection list is finished.

Cheers,
Sergei

Title: Re: inputRedirect syntax
Post by kai42 on Oct 28^th, 2007 at 3:13pm

Dear Sergei,

yes, I tried that before, but then I get:

"Error:Ran out of input in buffer during a redirected standard input read.
Current BL Command:Choice List for Parameters to test: with choice list:SKIP_NONE. Store result in paramSpec"

(.bf currently reads:

Code (]inputRedirect={};
inputRedirect["01"):

="Universal";
inputRedirect["02"]="C:\Program Files\HYPHY_Win32\clpP.fas";
inputRedirect["03"]="None";
inputRedirect["04"]="Default";
inputRedirect["05"]="Default";
inputRedirect["06"]="C:\Program Files\HYPHY_Win32\test.tre";
inputRedirect["07"]="Node15";
inputRedirect["08"]="";
ExecuteAFile("C:\Program Files\HYPHY_Win32\TemplateBatchFiles\TestBranchDNDS.bf", inputRedirect);

Title: Re: inputRedirect syntax
Post by Sergei on Oct 28^th, 2007 at 3:44pm

Dear Kai,

You need to add further options to the input list (both the names of the parameters to test and the empty string to terminate the selection). It helps to run through the analysis interactively and record every choice you make, to put them into the input list.

Cheers,
Sergei

Title: Re: inputRedirect syntax
Post by kai42 on Oct 28^th, 2007 at 4:11pm

Dear Sergei,
thanks - gotcha this time!
works perfectly!

Bests
Kai