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Thread: GUI Tool : An automated data conversion tool for genetics Data

  1. #1
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    GUI Tool : An automated data conversion tool for genetics Data

    An automated data conversion tool for connecting population genetics and genomics programs






    http://www.cmpg.unibe.ch/software/PGDSpider/


    Installing PGDSpider
    All necessary links and an installation instruction are also available on
    http://cmpg.unibe.ch/software/PGDSpider/
    or in the readme file.
    Installation Instructions
    1st step:
    Install the Java7 RE (or a newer version. At the moment it will not run under Java 9!)
    • Windows: download and install Java7 RE with following link:

    http://www.oracle.com/technetwork/ja...ads/index.html

    • Linux:
    o Ubuntu / Debian: Execute the following command as root user: "apt-get install openjdk-7-jre"
    o Other Linux distributions: http://www.oracle.com/technetwork/ja...ads/index.html
    Last edited by David Bush; 09-06-2020 at 06:35 PM.

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  3. #2
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    For confic>Option Use these files:

    http://www.mediafire.com/file/xa69co...i386-win32.zip

    Last edited by David Bush; 09-06-2020 at 09:09 PM.

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     anglesqueville (09-06-2020),  grumpydaddybear (09-08-2020)

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    If you encounter a memory size error
    Click on this file to run the software
    Open it in Notepad and edit it according to your system RAM

    http://www.mediafire.com/file/e9aar3...PGD_SPIDER.zip


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     grumpydaddybear (09-08-2020)

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    This is what I get when I try to run the .sh using java
    Code:
    java.lang.NoClassDefFoundError: org/w3c/dom/ls/DocumentLS
    	at java.base/java.lang.ClassLoader.defineClass1(Native Method)
    	at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
    	at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:802)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:700)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:623)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
    	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    	at org.apache.xerces.jaxp.DocumentBuilderImpl.<init>(Unknown Source)
    	at org.apache.xerces.jaxp.DocumentBuilderFactoryImpl.newDocumentBuilder(Unknown Source)
    	at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:861)
    	at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:773)
    	at org.apache.log4j.xml.DOMConfigurator.configure(DOMConfigurator.java:901)
    	at ch.unibe.iee.cmpg.pgdspider.PGDSpider.main(PGDSpider.java:17)
    Caused by: java.lang.ClassNotFoundException: org.w3c.dom.ls.DocumentLS
    	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
    	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    	... 15 more

  8. #5
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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    This is what I get when I try to run the .sh using java
    Code:
    java.lang.NoClassDefFoundError: org/w3c/dom/ls/DocumentLS
    	at java.base/java.lang.ClassLoader.defineClass1(Native Method)
    	at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
    	at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:802)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:700)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:623)
    	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
    	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    	at org.apache.xerces.jaxp.DocumentBuilderImpl.<init>(Unknown Source)
    	at org.apache.xerces.jaxp.DocumentBuilderFactoryImpl.newDocumentBuilder(Unknown Source)
    	at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:861)
    	at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:773)
    	at org.apache.log4j.xml.DOMConfigurator.configure(DOMConfigurator.java:901)
    	at ch.unibe.iee.cmpg.pgdspider.PGDSpider.main(PGDSpider.java:17)
    Caused by: java.lang.ClassNotFoundException: org.w3c.dom.ls.DocumentLS
    	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
    	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    	... 15 more
    I run on Windows operating system

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     Norfern-Ostrobothnian (09-13-2020)

  10. #6
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    Quote Originally Posted by David Bush View Post
    I run on Windows operating system
    Okay thanks, got it working on that. So do I need to create the fasta file using another program or are there any fastas than can be used as references?

  11. #7
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    How would one go about converting these two?
    https://drive.google.com/drive/folde...CC?usp=sharing
    The program is unable to parse the input and there's no fasta file.
    Last edited by Norfern-Ostrobothnian; 09-13-2020 at 03:36 PM. Reason: Fixed URLS

  12. #8
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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    How would one go about converting these two?
    https://drive.google.com/drive/folde...CC?usp=sharing
    The program is unable to parse the input and there's no fasta file.
    Please correct the link and say what format you want to convert it to

  13. #9
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    Quote Originally Posted by David Bush View Post
    Please correct the link and say what format you want to convert it to
    Fixed it. Ideally I would want to convert it straight to eigenstrat, but a PED or binary PED works too.

  14. #10
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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    Fixed it. Ideally I would want to convert it straight to eigenstrat, but a PED or binary PED works too.
    https://drive.google.com/drive/folde...LSDAla98KdGhCC
    To convert to eigenstrat format, you must introduce an external h19.fa file in the SPID section
    But I do not think this software is suitable for this conversion
    For example, it takes a long time to convert eigenstrat to bcf
    Last edited by David Bush; 09-13-2020 at 04:59 PM.

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