wcx2cytosure

This tool converts wisecondorx output to the “.CGH” format used by the commercial CytoSure Interpret Software by OGT (Oxford Gene Technology). CytoSure is made for displaying oligo array measurements. It works on a set of probes, which this tool emulates.

Usage

Requires an input .bins and .aberrations file from wisecondorx.

INSTALL:
    git  clone https://github.com/denrav99/wcx2cytosure.git
    cd wcx2cytosure
    pip install -e .

or use Singularity  

	singularity pull --arch amd64 library://ravinale/wcx2cytosure/wcx2cytosure:latest

RUNNING:
    
wcx2cytosure --wisecondorx_cov  <input.bins.bed> --wisecondorx_aberrations <input.aberrations.bed> --tiddit_cov <input.tiddit.tab> --out <output.cgh> --wcx_size <smallest aberration size (int)> (optional)

Notes on the file format

• CGH is in XML format. The company does not seem to have a schema file.

• The parser in CytoSure accepts reformatted XML files. This is ok:

  xmllint --format file.cgh > pretty.xml
  

• One probe can be made up of more than one spot:

  <probe ...>
    <spot ... />
    <spot ... />
  </probe>
  

• The probes in the file do not have to be sorted by chromosome and/or coordinate.

• There are <probe> elements without sequence, without chromosome name:

  <probe name="probename" sequence="">
    <spot index="56774" row="334" column="164" red="123.4" green="345.6" gSNR="1.0" rSNR="50.0" outlier="false"/>
  </probe>
  

• Coordinates are 1-based (since stop - start = 59 and length of sequence is 60)

• Removing the 'sequence' attribute does not work, but setting it to a fake one does

• Normalization segments look like this:

  <segment chrId="1" numProbes="10" start="7000" stop="1000000" average="-0.003"/>
  

• Segments can overlap each other

• Names "X" and "Y" are not used for the corresponding chromosomes. Instead, the X chromosome is stored as 23, they Y chromosome as 24 (in probes, segments and aberrations).