Révision 6e0010bc doc/sphinx_doc/build/text/tuto.txt

b/doc/sphinx_doc/build/text/tuto.txt
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the 53 samples is indentify by a uniq identifier. The file
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*CSV_SAMPLE_FILE* sums up this information.
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configurator.CSV_SAMPLE_FILE = None


  		





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   Path to cvs file that contains sample information.


  		





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We use a convention to link sample and Illumina fastq outputs.


  		





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Illumina output files of the sample *ID* will be stored in the


  		





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directory *ILLUMINA_OUTPUTFILE_PREFIX* + *ID*. For example, sample 41


  		





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outputs will be stored in the directory


  		





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*data/2012-09-05/FASTQ/Sample_Yvert_Bq41/*.


  		





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configurator.ILLUMINA_OUTPUTFILE_PREFIX = None


  		





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   Prefix for Illumina fastq output files.


  		





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For BY (resp. RM and YJM) we use following reference genome


  		





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*saccharomyces_cerevisiae_BY_S288c_chromosomes.fasta* (resp.


  		





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*saccharomyces_cerevisiae_rm11-1a_1_supercontigs.fasta* and


  		





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*saccharomyces_cerevisiae_YJM_789_screencontig.fasta*). The index


  		





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*FASTA_REFERENCE_GENOME_FILES* stores this information.


  		





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configurator.FASTA_REFERENCE_GENOME_FILES = None


  		





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   Dictionary where each fasta reference genomes is indexed by


  		





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   reference strain that it corresponds.


  		





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Each chromosome/contig is identify in the fasta file by an obscure


  		





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identifier. For example, BY chromosome I is identify by


  		





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*gi|144228165|ref|NC_001133.7|* when TemplateFilter is waiting for an


  		





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integer. So, we translate it. The index *FASTA_INDEXES* stores this


  		





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translation.


  		





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configurator.FASTA_INDEXES = None


  		





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   Dictionary of strain that indexes dictionaries where keys are


  		





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   chromosome reference from Fastq file and value are its


  		





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   correspondance for Templatefilter.


  		





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From a pragamatical point of view we discard some part of the genome


  		





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(repeated sequence etc...). The list of the black listed area is


  		





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explicitely detailled in *AREA_BLACK_LIST*.


  		





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configurator.AREA_BLACK_LIST = None


  		





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   Dictionary where keys are strain and values are black listed of


  		





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   geneome region.


  		





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For BY-RM (resp. BY-YJM and RM-YJM) genome sequence alignment we use


  		





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previously compute .c2c file


  		





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*data/2012-03_primarydata/BY_RM_gxcomp.c2c* (resp.


  		





  ......




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*NucleoMiner*, the old version of *NucleoMiner2* (http://www.ens-


  		





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lyon.fr/LBMC/gisv/NucleoMiner_Manual/manual.pdf).


  		





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configurator.C2C_FILES = None


  		





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   Dictionary where each strain combination indexes genome aligment.


  		





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*nucleominer* uses specific directory to work in, these are described


  		





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in *INDEX_DIR*, *ALIGN_DIR* and *LOG_DIR*.


  		





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