LandTextDump

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This function is not formally supported as part of any sales, it was developed as an internal tool. There is no GUI for this function, but the user can run it using Oshell or Run Script (Send To Queue).

Begin LandTextDump /Namespace=NgsLib;
Land "LandName";
AlvFolder "/path/ArrayLandVectorFiles";
MetaDataFile "/path/ArrayLandVectorFiles/MetaData.osobj";
ClinicalDataFile "/path/ArrayLandVectorFiles/LandName.cli";
SampleID "59M_OVARY";
CfgFile "/LandTextDump/LandName.cfg";
Options /Species=Human /OutputFolder="/LandTextDump/LandName" /RnaSeqQCFolder="/path/RnaSeq_QC" /BamFolder="/path/BAM"
/ExportAnnotations=True /ExportExpression=True /ExportCnv=True /ExportRnaSeqTranscript=True 
/ExportMutation=True /ExportFusion=True /ExportMethylation=True /ExportExonJunction=True /ExportExon=True /ExportClinicalData=True;
End;
  • MetaDataFile: please use the Omicsoft Object file: *.osobj file. User can add the meta table to a ArrayStudio Project and then save the object on the server.

LandMetaData.png

  • Species default is Human. Use Mouse for land land.
  • SampleID statement is optional. If not specified (ignoring the whole line), all samples in the MetaData object file will be exported.
  • ExportAnnotation includes both sample annotation and gene/transcript annotation
  • RnaSeqQCFolder is required if the QC dump is required. It must contain two sub folders:
    • AlignementQC: containing all .ngsqcm files for samples to be dumped.
    • AlignmentSummary: If there are paired-end samples, this folder will contain one file named "AlignmentSummaryPairedEnd.txt" (example file) with 24 columns of alignment statistics for all samples. If there are single-end samples, this file will contain one file named "AlignmentSummarySingleEnd.txt".
    • If all .bam files are on the same folder, we can use BamFolder option and it will use these *.summary.txt file directly. No AlignmentSummary file is required.
  • The output from this module will be the input for the Oracle/database input.
  • This module does not fully work for TCGA, which has a special exporter.
  • When the function is launched from Oshell, file path in the oscript needs to be absolute Linux path; when it is launched from Run Script (Send To Queue), the path needs to be virtual path in Array Server.