<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div apple-content-edited="true"><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; widows: auto;">Dear Dr. Jean Lobry,</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; widows: auto;"><br></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; widows: auto;">I confirmed that it worked properly as follows:</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; widows: auto;"><br></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; widows: auto;">-----------------------</div><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto;"><div><div>> whole.header.test <- </div><div>+ read.alignment(file = system.file("sequences/LTPs128_SSU_aligned_First_Two.fasta", </div><div>+ package = "seqinr"), format = "fasta", whole.header = TRUE)</div><div>> whole.header.test$nam</div><div>[1] "D50541\t1\t1411\t1411bp\trna\tAbiotrophia defectiva\tAerococcaceae" </div><div>[2] "KP233895\t1\t1520\t1520bp\trna\tAbyssivirga alkaniphila\tLachnospiraceae"</div></div><div>-----------------------</div><div><br></div><div>Thank you,</div><div><br></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Haruo Suzuki</div></div></div></div></div><br><div><div>On Feb 24, 2018, at 23:57, Jean Lobry <<a href="mailto:jean.lobry@univ-lyon1.fr">jean.lobry@univ-lyon1.fr</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear All,<br><br>I have commited a fix:<br><br><a href="http://seqinr.r-forge.r-project.org/src/appendix/releasenotes.pdf">http://seqinr.r-forge.r-project.org/src/appendix/releasenotes.pdf</a><br><br>available under the dev version of seqinr:<br><br>install.packages("seqinr", repos="http://R-Forge.R-project.org")<br><br>Best,<br><br>JLO<br><br>Le 23/02/2018 à 12:40, Jean Lobry a écrit :<br><blockquote type="cite">Dear Simon,<br>I was able to reproduce the bahaviour bescribed by<br>Haro Suzuki thereafter.<br>I've found the culprit in read.fasta() which is<br>called by read.alignment(). The name is indeed<br>truncated after the first space.<br>I'll commit a fix that doesn't break previous<br>code asap.<br>Best,<br>JLO<br>Le 22/02/2018 à 09:39, Haruo Suzuki a écrit :<br><blockquote type="cite">Dear Simon,<br><br>I hope all is well with you.<br><br>LTP datasets based on SILVA release 128 was downloaded from [Archive](https://www.arb-silva.de/no_cache/download/archive/living_tree/LTP_release_128/) using:<br>-----------------------<br> wget https://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_128/LTPs128_SSU/LTPs128_SSU_aligned.fasta.tar.gz <br> tar xvzf LTPs128_SSU_aligned.fasta.tar.gz<br>-----------------------<br><br>Here are FASTA header lines:<br>-----------------------<br>$grep "^>" LTPs128_SSU_aligned.fasta | head -n 2<br><blockquote type="cite">D50541 1 1411 1411bp rna Abiotrophia defectiva Aerococcaceae<br>KP233895 1 1520 1520bp rna Abyssivirga alkaniphila Lachnospiraceae<br></blockquote>-----------------------<br><br>The `read.alignment` function of SeqinR (Version: 3.4-5) did not get whole FASTA header lines (truncated descriptions probably because there are space " " between genus and species in organism names; e.g. "Abiotrophia defectiva" and "Abyssivirga alkaniphila") as follows:<br>-----------------------<br><blockquote type="cite">aln <- read.alignment("LTPs128_SSU_aligned.fasta", format = "fasta")<br>head(aln$nam, 2)<br></blockquote>[1] "D50541\t1\t1411\t1411bp\trna\tAbiotrophia"<br>[2] "KP233895\t1\t1520\t1520bp\trna\tAbyssivirga"<br>-----------------------<br><br># References<br>-----------------------<br>https://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_128/readme_LTP_SSUs128_LSUs123.pdf <br>LTPs128_SSU_aligned.fasta: multifasta alignments of type strains. The headers of the sequences accordingly stand for the following information: accession number, start and stop position, length, type of sequence, fullname_ltp, hi_tax_ltp. Also compressed for download as LTPs128_SSU_aligned.fasta.tar.gz<br>-----------------------<br><br>Yours sincerely,<br><br>Haruo Suzuki<br><br><br>On Nov 27, 2017, at 18:14, Simon Penel <simon.penel@univ-lyon1.fr> wrote:.<br><br></blockquote>_______________________________________________<br>Seqinr-forum mailing list<br>Seqinr-forum@lists.r-forge.r-project.org<br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum<br></blockquote><br></blockquote></div><br></body></html>