[GenABEL-dev] Fwd: Re: Small patch for probabel.pl (against 0.2.0)

[Marijn Verkerk]

Yurii,

FYI - our configuration file.

Marijn

On 08/31/2012 03:57 PM, Yurii Aulchenko wrote:
> Quite interesting and looks like going to
> be very useful for many people.
>
> Could you also please supply
> an example config file which makes use
> of your extensions (perhaps with some
> comments we can put as explanation to
> the manual).
>
> ----------------------
> Yurii Aulchenko
> (sent from mobile device)
>
> On 30 Aug 2012, at 10:57, Marijn Verkerk <m.verkerk at erasmusmc.nl 
> <mailto:m.verkerk at erasmusmc.nl>> wrote:
>
>> Small patch of probabel.pl <http://probabel.pl> for review!
>>
>> Regards,
>> Marijn
>>
>>
>> -------- Original Message --------
>> Subject: 	Re: Small patch for probabel.pl <http://probabel.pl> 
>> (against 0.2.0) - small correction
>> Date: 	Tue, 14 Aug 2012 16:15:39 +0200
>> From: 	Marijn Verkerk <m.verkerk at erasmusmc.nl>
>> To: 	L.C. Karssen <l.karssen at erasmusmc.nl>, yurii.aulchenko at gmail.com
>>
>>
>>
>> On 8/14/12 2:14 PM, Marijn Verkerk wrote:
>> > FYI
>> >
>> > This patch removes some redundancies in the code and makesprobabel.pl  <http://probabel.pl>  
>> > compatible with a bit more complicated cohort configuration, i.e.
>> > where cohorts are located at a location with multiple references to
>> > the chromosome, see attachments.
>> >
>> > Best wishes,
>> > Marijn
>> >
>>
>>
>>
>>
>>
>> <probabel.pl.patch>
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cohort,mlinfo_path,mldose_path,mlprobe_path,legend_path
# Use one line per cohort configuration.
#
# Use "_._chr_._" to specify a chromosome number in the configured paths. This can be used multiple times, e.g.: 
#
# mldose_path: /data/Cohort1/MachFiles/_._chr_._/mach_._chr_._-out.mldose 
#
# This will be replaced for chromosome 1: /data/Cohort1/MachFiles/1/1-out.mldose
#
#
RS1,/data/RS1/Imputed/OriginalFiles/_._chr_._/mach1.out.mlinfo,/data/RS1/Imputed/OriginalFiles/_._chr_._/Chr_._chr_._.fvi,/data/RS1/Imputed/OriginalFiles/merlin_._chr_._.collected.ped.out.mlprob,/data/RS-Legend/genotypes_chr_._chr_.__CEU_r22_nr.b36_fwd_legend.txt
RS2,/data/RS2/Imputed/OriginalFiles/._.chr._./mach1.out.mlinfo,/data/RS2/Imputed/OriginalFiles/_._chr._./Chr_._chr_._.fvi,/data/RS1/Imputed/OriginalFiles/mach1.out.mlprob,/data/RS-Legend/genotypes_chr_._chr_.__CEU_r22_nr.b36_fwd_legend.txt
RS3,/data/RS3/Imputed/OriginalFiles/._.chr._./mach1.out.mlinfo,/data/RS3/Imputed/OriginalFiles/_._chr._./Chr_._chr_._.fvi,/data/RS3/Imputed/OriginalFiles/mach1.out.mlprob,/data/RS-Legend/genotypes_chr_._chr_.__CEU_r22_nr.b36_fwd_legend.txt