Re: [Configobj-develop] questions about validation

[Michael F. <fuz...@vo...>]

  On 28/09/2010 05:27, Faheem Mitha wrote:
> 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

Hello Faheem,

I can't reproduce this error I'm afraid. I can create and validate 
config files using __many__ sections that contain __many__ sections.

If this is still an issue, can you create a *minimal* way to reproduce 
the error and attach it to a bug report on the ConfigObj bug tracker:

https://code.google.com/p/configobj/issues/list

All the best,

Michael Foord

> 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
>
> ********************************************************************
>
> [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"
>
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