AttachDesign

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[[Category:Import or Export Oscript]]
 
[[Category:Import or Export Oscript]]
Attaches a design table to a dataset.
 
  
[[Begin]] AttachDesign;
+
Attaches a design table to a dataset using a design.txt file.
  
[[Target]] DataSetName;
+
Begin AttachDesign;
 +
Target DataSetName;
 +
Project ProjectName;
 +
File "/user/jeff/demo_dir/design.txt";
 +
Mode ModeType=ColumnName, ModeType2=ColumnName2;
 +
Options  /Format=Txt /AttachServerAnnotation=False /Append=False /ChangeOrders=False /AttachByFilePath=False;
 +
End;
  
[[Project]] ProjectName;
 
  
[[File]] "/Path/DesignFileName";
+
Attaches a design table to a dataset using a sample registration *.osreg file.
  
[[Column Mode|Mode]] ModeType=ColumnName, ModeType2=ColumnName2;
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Begin AttachDesign;
 +
Target DataSetName;
 +
Project ProjectName; 
 +
Mode ModeType=ColumnName, ModeType2=ColumnName2;
 +
Options /AttachServerAnnotation=True /Append=False /ChangeOrders=False /AttachByFilePath=False;
 +
End;  
  
[[Options]]  /[[Format]]=Txt /[[AttachServerAnnotation]]=True /[[Append]]=False /[[ChangeOrders]]=False /[[AttachByFilePath]]=False;
 
  
[[End]];
+
Wrap the OScript up into PScript, to attache a generic design table to a dataset using a sample registration *.osreg file.
 +
 
 +
Begin AttachDesign /Run=;
 +
Project @ProjectName@;
 +
Target OmicData.FPKM_or_Count;
 +
File "@DesignFile@";
 +
Mode ModeType=ColumnName, ModeType2=ColumnName2;
 +
Options /Format=Txt /AttachServerAnnotation=False /Append=True /ChangeOrders=True /SuffixForDesignID=.Human /AttachByFilePath=False;
 +
End;
 +
 
  
 
*When [[AttachServerAnnotation]]=True, [[Format]] is not needed, nor is [[File]].
 
*When [[AttachServerAnnotation]]=True, [[Format]] is not needed, nor is [[File]].

Latest revision as of 22:58, 14 January 2020


Attaches a design table to a dataset using a design.txt file.

Begin AttachDesign; 
Target DataSetName; 
Project ProjectName; 
File "/user/jeff/demo_dir/design.txt"; 
Mode ModeType=ColumnName, ModeType2=ColumnName2; 
Options  /Format=Txt /AttachServerAnnotation=False /Append=False /ChangeOrders=False /AttachByFilePath=False; 
End;


Attaches a design table to a dataset using a sample registration *.osreg file.

Begin AttachDesign; 
Target DataSetName; 
Project ProjectName;  
Mode ModeType=ColumnName, ModeType2=ColumnName2; 
Options /AttachServerAnnotation=True /Append=False /ChangeOrders=False /AttachByFilePath=False; 
End; 


Wrap the OScript up into PScript, to attache a generic design table to a dataset using a sample registration *.osreg file.

Begin AttachDesign /Run=;
Project @ProjectName@;
Target OmicData.FPKM_or_Count;
File "@DesignFile@";
Mode ModeType=ColumnName, ModeType2=ColumnName2;
Options /Format=Txt /AttachServerAnnotation=False /Append=True /ChangeOrders=True /SuffixForDesignID=.Human /AttachByFilePath=False;
End;


  • When AttachServerAnnotation=True, Format is not needed, nor is File.
  • When AttachByFilePath=True, the design table will be attached by filename in file path, then the sample ID column will be used as ID column for the data. It is used for some functions such as import microarray data which uses CEL file names.
  • Another option is SuffixForDesignID, user can use /SuffixForDesignID=.Human to attach the design file to Xenograft human NgsData, and /SuffixForDesignID=.Mouse to attach the design file to Xenograft mouse NgsData.
  • If the table contains column ObservationID, the design file will be attached first, then AttachDesign (therefore all server pipelines) will change ID column to ObservationID column.