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HYPHY Package >> HyPhy feedback >> SimulateDataSet with partitions http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1175777847 Message started by wayne on Apr 5th, 2007 at 5:57am |
Title: SimulateDataSet with partitions Post by wayne on Apr 5th, 2007 at 5:57am
Hi Sergei, I am trying to simulate data under a simple partitioned model. the test scenario has four partitions (each of 50 aa), where the same model and tree is set for each partition (model0 - model3, tree0 -tree3). the script returns a dataset, yet when looking at the category classes under which sites were simulated i get the ff:
site # omega_class 38 0.0250114 39 0.0250114 40 1 41 0.0250114 42 0.0250114 43 0.0250114 44 0.0250114 45 0.0250114 46 0.0250114 47 1 48 0.0250114 49 0.0250114 50 0 51 0 52 0 53 0 which up until site 50 makes sense, since the catvar is (0.025, 1) @ frequencies (0.96, 0.04). However, sites 50-149 return 0's consistent with partitions 1 & 2. Partition 3 again returns correct values. any suggestions/comments would be appreciated. thanks ./w batchfile requires a 600 bp sequence file in order for manual partitioning to work. Code (]_Genetic_Code = { {14,/*AAA*/ 13,/*AAC*/ 14,/*AAG*/ 13,/*AAT*/ 7, /*ACA*/ 7, /*ACC*/ 7, /*ACG*/ 7, /*ACT*/ 19, /*AGA*/ 5, /*AGC*/19, /*AGG*/ 5, /*AGT*/ 2, /*ATA*/ 2, /*ATC*/ 3, /*ATG*/ 2, /*ATT*/ 12,/*CAA*/ 11,/*CAC*/ 12,/*CAG*/ 11,/*CAT*/ 6, /*CCA*/ 6, /*CCC*/ 6, /*CCG*/ 6, /*CCT*/ 19,/*CGA*/ 19,/*CGC*/ 19,/*CGG*/ 19,/*CGT*/ 1, /*CTA*/ 1, /*CTG*/ 1, /*CTC*/ 1, /*CTT*/ 16,/*GAA*/ 15,/*GAC*/ 16,/*GAG*/ 15,/*GAT*/ 8, /*GCA*/ 8, /*GCC*/ 8, /*GCG*/ 8, /*GCT*/ 20,/*GGA*/ 20,/*GGC*/ 20,/*GGG*/ 20,/*GGT*/ 4, /*GTA*/ 4, /*GTC*/ 4, /*GTG*/ 4, /*GTT*/ 10,/*TAA*/ 9, /*TAC*/10,/*TAG*/ 9, /*TAT*/ 5, /*TCA*/ 5, /*TCC*/ 5, /*TCG*/ 5, /*TCT*/ 10,/*TGA*/ 17,/*TGC*/ 18,/*TGG*/ 17,/*TGT*/ 1, /*TTA*/ 0, /*TTC*/ 1, /*TTG*/ 0 /*TTT*/ } }; GeneticCodeExclusions = "TAA,TAG,TGA"; function CodonFrequencies ( nucFreqMatrix, mSize ) /* Modified from Kosakovsky Pond */ { PIStop = 1.0; result = { mSize, 1 }; hshift = 0; for ( h = 0; h < 64; h = h + 1 ) { first = h$16; second = h%16$4; third = h%4; if ( _Genetic_Code[ h ):
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Title: Re: SimulateDataSet with partitions Post by Sergei on Apr 9th, 2007 at 9:23am
Dear Wayne,
Looks like there is a bug in HyPhy when it tries to populate simulated rates for multiple partitions (I am pretty sure the rates themselves are drawn accurately - just that the values are not written properly) - I'll check into it today and try to roll a fix into the next build. Cheers, Sergei |
Title: Re: SimulateDataSet with partitions Post by Sergei on Apr 9th, 2007 at 11:57am
Dear Wayne,
Good catch: HyPhy had an internal indexing bug which would not write simulated rates to appropriate cells in the rate matrix for codon data. I fixed the problem - look for the next build to work properly. Thanks! Sergei |
Title: Re: SimulateDataSet with partitions Post by wayne on Apr 10th, 2007 at 1:02am
thanks ./w
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