<ul style="font-family: courier new,monospace;"><li><font size="2"><a href="http://lists.r-forge.r-project.org/pipermail/seqinr-forum/2009q4/000057.html">[Seqinr-forum] suggested SeqinR function for printing a list of sequences to a fasta file
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<i>Coghlan, Avril </i><i>Thu Dec 10 17:51:11 CET 2009</i></font></li></ul><font style="font-family: courier new,monospace;" size="2">Dear Jean and Simon,<br><br>I took Jean's example from the above thread,<br></font><pre style="font-family: courier new,monospace;">
<font size="2">> library(seqinr)<br>> choosebank("genbank")<br>> query("humtRNAs", "SP=homo sapiens AND M=TRNA") <br>> myseqs <- getSequence(humtRNAs) <br>> mynames <- getName(humtRNAs) <br>
> write.fasta(myseqs,mynames, file = "myseqs.fasta") ######<br><br>and made a few changes, but after those changes my output was no <br>longer a normal FASTA file: instead, it first had all header lines <br>bunched together, then all the DNA sequences concatenated in one <br>
block. Here are the commands I used:<br><br>library(seqinr)<br>choosebank("genbank")<br>query("mydat", "AU=Matute")<br>modifylist("mydat",operation=">613")<br>modifylist("mydat",operation="<615") <br>
myseqs <- getSequence(mydat)<br>mynames <- getName(mydat)<br>write.fasta(myseqs,mynames, file = "myseqs.fasta")<br><br>I've tried repeating this example many times under the same conditions <br>(new R console, on Mac OSX). The problem seem to be intermittent, <br>
because very rarely I do get the normal FASTA output, but then the <br>next time everything segregates again. Do you have an idea what might <br>be causing this?<br><br>Many thanks for your help,<br><br>Best regards,<br><br>
Oliver Clay<br><br></font></pre><br>