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<div dir="ltr">Hi there,<div><br></div><div>I would like to calculate Fst on 1292 genes between 5 populations.</div><div>So I have 1292 fasta files containing around 30 individual sequences.</div><div>I saw there is a pairwise.fst function that could be what I want. </div><div><br></div><div>But before that I need to use the fasta2bin function in order to read alignments form my fasta files.</div><div>The problem is that when I apply this function, for a fasta file containing 30 alignments, the processing seems to be very very long.</div><div><br></div><div>Here are my script and the results:</div><div>--------------------------------------------------------------------------------</div><div><div><b>library(adegenet)</b></div><div><b>res <- fasta2DNAbin("/Users/abessy/Documents/SA_without_N/DSPR_without_N/140up_Chr3R_14124163_14125548.fas_without_N.fas")</b></div></div><div><b><br></b></div><div><p style="font-size: 14px; font-family: Menlo;">> source("fasta.R")</p>
<p style="font-size: 14px; font-family: Menlo;"><b>Loading required package: ade4</b></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo;"><b> /// adegenet 2.0.1 is loaded ////////////</b></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo;"><b> > overview: '?adegenet'</b></p>
<p style="font-size: 14px; font-family: Menlo;"><b> > tutorials/doc/questions: 'adegenetWeb()' </b></p>
<p style="font-size: 14px; font-family: Menlo;"><b> > bug reports/feature resquests: adegenetIssues()</b></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo;"> Converting FASTA alignment into a DNAbin object... </p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo;"> Finding the size of a single genome... </p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p></div><div><b>-----------------------------------------------------------------------------------</b></div><div><b><br></b></div><div>I tried with the fasta2genlight function and the processing seems to be very very long too, even with using the parallel parameter:</div><div>-----------------------------------------------------------------------------------</div><div><div><b>library(adegenet)</b></div><div><b>library(parallel)</b></div><div><b>res1<- fasta2genlight("/Users/abessy/Documents/SA_without_N/DSPR_without_N/140up_Chr3R_14124163_14125548.fas_without_N.fas",parallel=TRUE)</b></div></div><div><b><br></b></div><div><p style="font-size: 14px; font-family: Menlo;">> source("fasta.R")</p>
<p style="font-size: 14px; font-family: Menlo;"><b>Loading required package: ade4</b></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo;"><b> /// adegenet 2.0.1 is loaded ////////////</b></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo;"><b> > overview: '?adegenet'</b></p>
<p style="font-size: 14px; font-family: Menlo;"><b> > tutorials/doc/questions: 'adegenetWeb()' </b></p>
<p style="font-size: 14px; font-family: Menlo;"><b> > bug reports/feature resquests: adegenetIssues()</b></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo;"> Converting FASTA alignment into a genlight object... </p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p>
<p style="font-size: 14px; font-family: Menlo; min-height: 16px;">---------------------------------------------------</p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;">Have you an idea why it is so long ?</p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;">I have a iMac. </p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;">I attached my fasta file.</p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;">Best wishes</p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;"><br></p><p style="font-size: 14px; font-family: Menlo; min-height: 16px;">Adrien</p></div><div><br></div><div><br></div></div>
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