[Configobj-develop] questions about validation

[Faheem M. <fa...@em...>]

Hi,

I'm having problems writing a validation file.

For the config below, what I would like to do is something like

[__many__]
annotfile = string

         [[__many__]]
         phenofiles = string_list
         genofile = string
         test_genofile = string

[affy6]
fidlist = string_list

[illumina]
rsidlist = string_list

but I can't because I get complaints of duplicate sections. I've no idea 
why trying to do this should be a problem. It seems quite reasonable to 
me.  The following (with repeated checks for affy6 and illumina)

[affy6]
annotfile = string
fidlist = string_list

       [[__many__]]
         phenofiles = string_list
         genofile = string
         test_genofile = string

[illumina]
annotfile = string
rsidlist = string_list

         [[__many__]]
         phenofiles = string_list
         genofile = string
         test_genofile = string

works, but having all this duplication (eg. identical __many__ sections 
for both the affy6 and illumina sections) seems kind of dotty.

So, how can I nest a many inside a many and still have specific sections 
at an upper level? The idea is to avoid duplication as much as possible.

                                                          Thanks, Faheem

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[affy6]
annotfile = "/data/snppy/Hapmap6.0/Geno/GenomeWideSNP_6.na29.annot.csv"
fidlist = SNP_A-1780419, SNP_A-1780418, SNP_A-1780415, SNP_A-1780414, SNP_A-1780413, SNP_A-8493668, SNP_A-8497683, SNP_A-8499914, SNP_A-8515633, SNP_A-8558729, SNP_A-8580441, AFFX-SNP_11601946, SNP_A-1884440, AFFX-SNP_9061467, SNP_A-2254440
     [[hapmap]]
     phenofiles = /data/snppy/Hapmap6.0/Pheno/hapmappheno_909.csv,
     genofile = /data/snppy/Hapmap6.0/Geno/birdseed-v2.calls.txt
     test_genofile = birdseed-v2.calls.trunc.txt
     [[btsnp]]
     phenofiles = /data/snppy/btsnp/WG4_BreastBmt.csv, /data/snppy/btsnp/WG4_demog.csv
     genofile = /data/snppy/btsnp/birdseed.calls.txt
     test_genofile = birdseed.calls.trunc.txt
[illumina]
annotfile = "/data/snppy/Hapmap610/Human610-Quadv1_B.csv"
rsidlist = rs8179466, rs943918, rs798075, rs4650275, rs7552097
     [[ceu]]
     phenofiles = /data/snppy/Hapmap610/ceupheno.csv,
     genofile = "/data/snppy/Hapmap610/Human610-Quadv1_CEU_Genotype_Report.txt"
     test_genofile = "Human610-Quadv1_CEU_Genotype_Report.trunc.txt"
     [[chbjpt]]
     phenofiles = "/data/snppy/Hapmap610/chbjptpheno.csv",
     genofile = "/data/snppy/Hapmap610/Human610-Quadv1_CHBJPT_Genotype_Report.txt"
     test_genofile = "Human610-Quadv1_CHBJPT_Genotype_Report.trunc.txt"