Global parameters

The global section of the design file is composed of 6 parameters (3 are optional):

Parameter Type Value Optional Description
formatversion String 1.1 No The 1.1 version is currently the only version of the format supported by Teolenn.
startposition Integer 0 or 1 No The way the first base is numbered.
oligolenght Integer Must be > 0 No The length of the oligonucleotide to design
oligointervallenght Integer Must be >= 0 Yes, if omitted oligointervallenght will be set to 0. The interval of length of oligonucleotides. The lengths of oligonucleotides generated by Teolenn will be oligolenght ± oligointervallenght.
genomefile String A relative or an absolute path Yes, can be overrided by the second argument of teolenn.sh The path to the genome file. All the sequences must be in one file in fasta format.
genomemaskedfile String A or an absolute relative path Yes, can be overrided by the third argument of teolenn.sh The path to the masked genome file. All the sequences must be in one file in fasta format.
outputdir String A relative or an absolute path Yes, can be overrided by the 4th argument of teolenn.sh. If none value is set in design file or in command line, the value is set to the current directory. The path to the output directory

The following source show a sample the global section of design file:

<design>
	<formatversion>1.1</formatversion>
	<startposition>0</startposition>
	<oligosize>60</oligosize>

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