flashtop
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Feed your monkey!
Posts: 18
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hi guys
Using the GTK hyphy MP build, the batch file TEST.BF below shows that either the HarvestFrequencies or CreateFilter command does not cut out the stop codons. Both codon frequency vectors are 64x1 and are identical.
### test.bf #### DataSet PF01226 = ReadDataFile("/home/flash/Jedi/pipeline/drumline/coli-dN-high.fasta"); DataSetFilter entireF_nostops = CreateFilter(PF01226,3,"","","TAA,TAG,TGA"); DataSetFilter entireF_withstops = CreateFilter(PF01226,3); HarvestFrequencies(obsFreqs,entireF_nostops,3,3,1); HarvestFrequencies(estFreqs,entireF_withstops,3,3,1); fprintf(stdout, obsFreqs, estFreqs);
The message log says that:
"More than 50% of characters in the data are not in the alphabet."
Perhaps the filter does not count the alphabet exclusions as codons but rather as nucleotides??
The Commands work fine on nucleotide data, as run with TEST2.BF:
### test2.bf ### DataSet PF01226 = ReadDataFile("/home/flash/Jedi/pipeline/drumline/coli-dN-high.fasta"); DataSetFilter entireF_nostops = CreateFilter(PF01226,1,"","","T"); DataSetFilter entireF_withstops = CreateFilter(PF01226,1); HarvestFrequencies(obsFreqs,entireF_nostops,1,1,1); HarvestFrequencies(estFreqs,entireF_withstops,1,1,1); fprintf(stdout, obsFreqs, estFreqs);
I've put the fasta file I'm using through the StripStopCodons.bf under Standard Analyses which said that no stop codons were present. I can't attach it but I can mail it to you if you need it.
Would you guys mind checking it out if you have time?
Thanx Gordon
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