Jose_Patane
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Posts: 26
Brazil
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As always, thks again, your code worked out - branches and ML estimates are ok now!
Anyway, for future analysis I'd like to know what I've done wrong, so here's how I was doing it:
- position of "gene_231" (meaning the 1st codon position starts on site #2) in the concatenated sequence of all the genes (not 0-indexed, this is actually the raw position in the alignment): 2741-3119 (379 bp).
Here's the code I had formerly used to partition the data into codon positions:
------------------------------------------------------------------ DataSet All_seqs= ReadDataFile("my_concatenated_data");
DataSetFilter gene_231 = CreateFilter (All_seqs,1,"2740-3118");
DataSetFilter filteredData1 = CreateFilter (gene_231,1,"<010>"); DataSetFilter filteredData2 = CreateFilter (gene_231,1,"<001>"); DataSetFilter filteredData3 = CreateFilter (gene_231,1,"<100>");
..... ..... .....
fprintf (stdout,"n_sites_1st = ", filteredData1.sites); fprintf (stdout,"n_sites_2nd = ", filteredData2.sites); fprintf (stdout,"n_sites_3rd = ", filteredData3.sites);
..... ..... .....
-------------------------------------------------------------------------
... with results:
"n_sites_1st = 126 n_sites_2nd = 126 n_sites_3rd = 126"
Like I had said, the starting sequences at '312' and '123' return proper results using this kind of code... can you help me figuring out what went wrong?
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