The design file

The design file (usually named as design.xml) is the file where all the parameters of a design will be set. This file use the XML syntax and is divided in 8 sections :

  • The global parameters. Set the main parameter of the design (length of oligonucleotides, path to the files...).
  • The constant section. This section allow to set constants that will be used in the whole design file. This section is optional.
  • The sequencefilters section. This section enable or not the creation of all the oligonucleotides. This section is also optional.
  • The sequencefilters section. This section define the filters on all the oligonucleotides generated.
  • The measurements section. This section define the measurement to compute on the filtered oligonucleotides.
  • The measurementfilters section. This section define the filters based on measurements to remove oligonucleotides.
  • The selector section. This part of the file set the parameters to select the bests oligonucleotides.
  • The outputs section. This last part of the file set the parameters of the output(s) of selected oligonucleotides. If this section is absent, the default output will be used.

All the tags must be in lower case. The following source show the structure of a typical design.xml file:

<design>
    <formatversion>1.1</formatversion>
    
    <startposition>0</startposition>
    <oligolength>60</oligolength>
    <oligointervallength>0</oligointervallength>

    <genomefile>Ca21_chromosomes2.fasta</genomefile>
    <genomemaskedfile>Ca21_chromosomes2.fasta.allmasked</genomemaskedfile>
    <outputdir>/home/jourdren/tmp/candida_design</outputdir>
    
    <constants>
    ...
    </constants>

    <sequencecreator/>

    <sequencefilters>
    ...
    </sequencfilters>
    
    <measurements>
    ...
    </measurements>
    
    <measurementfilters>
    ...
    </measurementfilters>
    
    <selector>
    ...
    </selector>
    
    <outputs>
    ...
    </outputs>
</design>

Note that all pluggable elements (sequencefilters, measurements, measurementsfilter, selectors, outputs) names, all parameters names and constants names are case insensible in the design file.

Skip steps

All the phases from sequences creation to selection of the best oligonucleotides can be skipped. To skip a phase set the skip attribute to true in the phase tag. As an example the following fragment of design file will skip the selection phase:

    <selector skip="true">
    ...
    </selector>

Built-in variables

In parameters sections of the design file, you can use the following built-in variables as values for parameters:

  • ${startPosition}: Contains the way the first position of the sequence is referred to. Can take value 0 or 1.
  • ${genomefile}: Contains the path to the genome file.
  • ${genomemaskedfile}: Contains the path to the genome masked file.
  • ${outputdir}: Contains the path to the output directory.
  • ${oligolenght}: Contains the length of the oligonucleotides.