HyPhy message board - Batch files

	Welcome, Guest. Please Login

Home

Help

HyPhy message board › Methodology Questions › How to › Batch files

(Moderators: Sergei, Simon)

‹ Previous Topic | Next Topic ›

Pages: 1

Send Topic

Batch files (Read 2647 times)

jhughes

YaBB Newbies

Offline

Feed your monkey!

Posts: 5

Batch files
Aug 8^th, 2011 at 9:05am

Hi,

I'm new to HYPHY. I am trying to create batch files for processing 100s of files. So far I have managed to do a batch for testing the best model using AIC. Now I want to use SLAC to calculate dN/dS and whether there are any sites under selection using the best model selected using modeltest. The QuickSelectionDetection.bf requests a ModelString. What is the best way to get and use the output from the MotelTest batch file and in particular the ModelString to use in the QuickSelectionDetection batch files.

Cheers,
Joseph

IP Logged

Sergei

YaBB Administrator

Offline

Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male

Re: Batch files
Reply #1 - Aug 9^th, 2011 at 4:17pm

Hi Joseph,

You probably want to use a wrapper file. Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

modelStrings[chosenMatrix]

,

otherwise it will be in
Code:

modelStrings[aicMatrix]

In your wrapper file do something like

Code:

...

for (...)
{
     ...

     ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "ModelTest.bf", modelTestOptions);

     slacOptions = {};
     ...

     slacOptions [".."] = modelStrings[aicMatrix];

     ...

 ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "QuickSelectionDetectiob.bf", slacOptions);

}

Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

WWW

IP Logged

jhughes

YaBB Newbies

Offline

Feed your monkey!

Posts: 5

Re: Batch files
Reply #2 - Aug 10^th, 2011 at 12:49am

In the end I succeeded by doing this, where every other line of the list of files provided is the ModelString from model test.

Code:

/* This is a HY-PHY Batch File for producing the SLAC analyses.

  
*/

fileToExe = HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "QuickSelectionDetection.bf";

/* a  list of file paths */
SetDialogPrompt ( "Provide a list of files to process:" );
fscanf ( PROMPT_FOR_FILE, "Lines", _inDirectoryPaths );

fprintf (stdout, "[READ ", Columns (_inDirectoryPaths), " file path lines]\n");

/* the options passed to the GUI are encoded here */
inputRedirect = {};
inputRedirect["01"]="Universal";
inputRedirect["02"]="New Analysis";
inputRedirect["04"]="Custom";
inputRedirect["08"]="Estimate + CI";
inputRedirect["09"]="Single Ancestor Counting";
inputRedirect["10"]="Full tree";
inputRedirect["11"]="Averaged";
inputRedirect["12"]="Approximate";
inputRedirect["13"]="0.05";
inputRedirect["14"]="Export to File";
inputRedirect["16"]="Skip";

for ( _fileLine = 0; _fileLine < Columns ( _inDirectoryPaths ); _fileLine = _fileLine + 2 ) {

	inputRedirect [ "03" ]	= "/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/UniqsNoStop/"+_inDirectoryPaths[ _fileLine ]+".fasta";
	inputRedirect [ "05" ]	= _inDirectoryPaths[ _fileLine + 1];
	inputRedirect [ "06" ]	= "/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/trees/"+_inDirectoryPaths[ _fileLine ]+".tre";
	inputRedirect [ "07" ]	= "/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/SLAC/"+_inDirectoryPaths[ _fileLine ]+".bf";
	inputRedirect [ "15" ]	= "/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/SLAC/"+_inDirectoryPaths[ _fileLine ]+".out";
	ExecuteAFile ( fileToExe, inputRedirect );
}

I will try your more elegant approach.

Cheers,
Joseph

IP Logged

jhughes

YaBB Newbies

Offline

Feed your monkey!

Posts: 5

Re: Batch files
Reply #3 - Aug 10^th, 2011 at 3:31am

And just in case someone finds this useful, here is the more elegant way that Sergei suggested: Code:

/* a  list of file paths */
SetDialogPrompt ( "Provide a list of files to process:" );
fscanf ( PROMPT_FOR_FILE, "Lines", _inDirectoryPaths );

fprintf (stdout, "[READ ", Columns (_inDirectoryPaths), " file path lines]\n");


for ( _fileLine = 0; _fileLine < Columns ( _inDirectoryPaths ); _fileLine = _fileLine + 1 ) {
inputRedirect = {};
inputRedirect["01"]="Universal";
inputRedirect["02"]="/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/UniqsNoStop/"+_inDirectoryPaths[ _fileLine ]+".fasta";
inputRedirect["03"]="/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/trees/"+_inDirectoryPaths[ _fileLine ]+".tre";
inputRedirect["04"]="4";
inputRedirect["05"]="AIC Test";
inputRedirect["06"]="/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/modeltest/"+_inDirectoryPaths[ _fileLine ]+".out";
ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles"+ DIRECTORY_SEPARATOR+"ModelTest.bf", inputRedirect);

inputRedirect = {};
inputRedirect["01"]="Universal";
inputRedirect["02"]="New Analysis";
inputRedirect["03"]="/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/UniqsNoStop/"+_inDirectoryPaths[ _fileLine ]+".fasta";
inputRedirect["04"]="Custom";
inputRedirect["05"]=modelStrings[aicMatrix];
inputRedirect["06"]="/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/trees/"+_inDirectoryPaths[ _fileLine ]+".tre";
inputRedirect["07"]="/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/SLAC/"+_inDirectoryPaths[ _fileLine ]+".bf";
inputRedirect["08"]="Estimate + CI";
inputRedirect["09"]="Single Ancestor Counting";
inputRedirect["10"]="Full tree";
inputRedirect["11"]="Averaged";
inputRedirect["12"]="Approximate";
inputRedirect["13"]="0.05";
inputRedirect["14"]="Export to File";
inputRedirect["15"]="/Users/jhughes/Documents/PabloProjects/HYPHYanalyses/SLAC/"+_inDirectoryPaths[ _fileLine ]+".out";
inputRedirect["16"]="Skip";

ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles"+
DIRECTORY_SEPARATOR+"QuickSelectionDetection.bf", inputRedirect);

}

Joseph

IP Logged

Pages: 1

Send Topic

‹ Previous Topic | Next Topic ›

« Home

‹ Board

Top of this page