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Command Line Output Folder Options In Haploview

Hi all,

I am trying to run a batch file with the Haploview command line interface but I can't seem to figure out how to get my output into a folder as individual files.

java -jar Haploview.jar -n -out Results -batch file_test.txt -blockoutput ALL -minMAF 0.05 -check -svg -pairwiseTagging 
java -jar Haploview.jar -n -out \Results\ -batch file_test.txt -blockoutput ALL -minMAF 0.05 -check -svg -pairwiseTagging 
java -jar Haploview.jar -n -out "\Results\" -batch file_test.txt -blockoutput ALL -minMAF 0.05 -check -svg -pairwiseTagging

None of these seem to give the desired result. Any suggestions will be greatly appreciated.

Thanks.

-Avoks

haploview
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updated by Mwangana • Mwangana • written by Avoks • Avoks

What exactly happens when you run the command? Does the results folder exist and spelled right (case sensitive)?

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written by Damian Kao Damian Kao

Hi Dk. The folder does exist. The first option creates Results.TAGS in the working directory, one of the files to be created per file in the batch input and just overwrites it over and over so there are results for just one entry. The second and third options are similar. They create a file simply called ".TAGS" in the Results folder and overwrites it just like the first option. The input for the -out argument is meant to be <fileroot> and I think that's where the Results folder is located.

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written by Avoks • Avoks

Sorted...perl script.

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written by Avoks • Avoks

1 answer

You were very close. Sorry for answering so late; the following should work:

java -jar Haploview.jar -n -out "Results/myanalysis" -batch file_test.txt -blockoutput ALL -minMAF 0.05 -check -svg -pairwiseTagging

This will create your output files in the "Results" directory, all having the prefix "myanalysis":

$: ls Results
myanalysis.4GAMblocks  myanalysis.CHECK  myanalysis.GABRIELblocks  myanalysis.LD.SVG  myanalysis.SPINEblocks  myanalysis.TAGS  myanalysis.TESTS
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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

@Giovanni M Dall'Olio, I have tried this command. It works perfectly but when I replace "-svg" by "-png" , it throws errors such as: Exception in thread "main" java.lang.NoSuchMethodError: 'void java.lang.System.runFinalizersOnExit(boolean)' at com.sun.jimi.core.Jimi.<clinit>(Jimi.java:128) at edu.mit.wi.haploview.HaploText.processFile(HaploText.java:1680) at edu.mit.wi.haploview.HaploText.processTextOnly(HaploText.java:1369) at edu.mit.wi.haploview.HaploText.<init>(HaploText.java:245) at edu.mit.wi.haploview.HaploView.main(HaploView.java:1600)

How can I get Haploview to output .PNG without these errors?

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written by Mwangana • Mwangana

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