Release export wizard

[Nicklas Nordborg]

Implement a wizard for creating all files that should be included in a release. Th wizard should take an item list with raw bioassays as input and produce a lot of files. Unless noted, all files are tab-separated text files.

• Transcript data (in folder dataTables/transcriptDataTable):
  • tidmatrix.features.txt: Array design features with some annotations. The first line is a header line:
    • id, geneSymbol, refSeq, protAcc, description, chr, entrez.
    • Rows are sorted by ID.
    • All raw bioassays in the input list must use the same array design.
  • tidmatrix_data.txt: FPKM values for all raw bioassays. Each row represents a feature and each column a raw bioassay.
    • The first line is a header line with raw bioassay names.
    • The first column contains the feature ID.
    • Same order of rows as the tidmatrix.features.txt.
  • tidmatrix_FPKM_conf_hi.txt, tidmatrix_FPKM_conf_lo.txt, tidmatrix_FPKM_status.txt: More data files similar to the tidmatrix_data.txt file but with the FPKM_conf_hi, FPKM_conf_lo and FPKM_status values.

• Gene data (in folder dataTables/geneDataTable):
  • genematrix_data.txt: Sum of FPKM values per gene symbol.
    • The first line is a header line with raw bioassay names.
    • The first column is the gene symbol (in no particular alphabetical order).
  • is.NM.gene.txt: TRUE/FALSE flag for each gene indicating if the refSeq ID starts with NM_ or not.
    • No header line.
    • First column is the line number (in this file, add +1 for getting the line number in genematrix_data.txt).
    • Second column is TRUE or FALSE.

• Cohort data (in folder cohortTables):
  • TODO

• README files
  • TODO

[Nicklas Nordborg]

For efficient calculations it is desirable to process the data gene symbol by gene symbol. Thus, the data must come sorted in gene symbol order.