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Red Hat Bugzilla – Attachment 318020 Details for
Bug 464460
Review Request: pypop - Python for Population Genomics
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sample.ini (configuration file)
sample.ini (text/plain), 1.51 KB, created by
Alex Lancaster
on 2008-09-29 22:54:14 UTC
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Description:
sample.ini (configuration file)
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Creator:
Alex Lancaster
Created:
2008-09-29 22:54:14 UTC
Size:
1.51 KB
patch
obsolete
>;; comment out or change as desired >;; 1 = true, 0 = false > >[General] >debug=0 > >[ParseGenotypeFile] >untypedAllele=**** > >;; designates field name that holds allele data >alleleDesignator=* > >;; valid fields for sample data block >validSampleFields=*a_1 > *a_2 > *c_1 > *c_2 > *b_1 > *b_2 > *dra_1 > *dra_2 > *drb1_1 > *drb1_2 > *dqa1_1 > *dqa1_2 > *dqb1_1 > *dqb1_2 > *dpa1_1 > *dpa1_2 > *dpb1_1 > *dpb1_2 > >[HardyWeinberg] >lumpBelow=5 > >[HomozygosityEWSlatkinExact] >;; use section if the Monte Carlo approximation to the Slatkin exact >;; Ewens-Watterson test should be run >numReplicates=10000 > >[Emhaplofreq] > >;; comma (',') separated haplotypes blocks for which to estimate >;; haplotypes, within each "block", each locus is separated by colons >;; (':') e.g. dqa1:dpb1,drb1:dqb1, means to est. of haplotypes for >;; 'dqa1' and 'dpb1' loci followed by est. of haplotypes for 'drb1' >;; and 'dqb1' loci. A wildcard entry '*' means estimate haplotypes >;; for the entire loci as specified in the original file column order >;;lociToEstHaplo=a:b:drb1,a:b:c,drb1:dqa1:dpb1,drb1:dqb1:dpb1 > >;; analogous to `lociToEst' except for linkage disequilibrium (LD) >;;lociToEstLD= > >;; pairwise estimates can be run in two ways: with or without >;; permutation test. > >;; if LD *and* permutation test for all pairwise loci are desired, >;; then set both options '1' (true); the separate >;; 'allPairwiseLDWithHaplo' and 'allPairwiseLDWithHaploWithPermu' >;; options are now obsolete > >;; estimate LD for all pairwise loci? >allPairwiseLD=1 > >;; with permutation test? >allPairwiseLDWithPermu=0
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bug 464460
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