<html><head></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div dir="ltr" id="yui_3_16_0_ym19_1_1495618982395_25461">Hi Peter,</div><div id="yui_3_16_0_ym19_1_1495618982395_25483" dir="ltr"><br></div><div id="yui_3_16_0_ym19_1_1495618982395_25484" dir="ltr">Thanks for your reply. Yes I have a fully aligned sequence in the FASTA file, with dashes showing the indels.</div><div id="yui_3_16_0_ym19_1_1495618982395_25580" dir="ltr"><br></div><div id="yui_3_16_0_ym19_1_1495618982395_25581" dir="ltr">Best,</div><div dir="ltr">-Michiel<br></div> <div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font face="Arial" size="2"> On Wednesday, May 24, 2017 6:22 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:<br></font></div> <br><br> <div class="y_msg_container"><div dir="ltr">Hi Michiel,<br clear="none"><br clear="none">Both use SeqRecord objects internally, so it ought to be possible.<br clear="none">Presumably you would assume the query and match coordinates<br clear="none">were for the full aligned sequence in the FASTA file?<br clear="none"><br clear="none">Peter<br clear="none"><div class="yqt1271370800" id="yqtfd69443"><br clear="none">On Fri, May 19, 2017 at 9:41 AM, Michiel de Hoon <<a shape="rect" ymailto="mailto:mjldehoon@yahoo.com" href="mailto:mjldehoon@yahoo.com">mjldehoon@yahoo.com</a>> wrote:<br clear="none">> Dear all,<br clear="none">><br clear="none">> Is there some easy way to convert a Bio.Align.MultipleSeqAlignment object<br clear="none">> into a Bio.SearchIO.QueryResult ?<br clear="none">> The reason I'm asking is that I am trying to convert a pairwise sequence<br clear="none">> alignment in Fasta format into PSL format.<br clear="none">> I am hoping to read the Fasta file with Bio.AlignIO, then convert the<br clear="none">> Bio.Align.MultipleSeqAlignment object into a Bio.SearchIO.QueryResult<br clear="none">> object, and write it out as PSL using Bio.SearchIO.<br clear="none">><br clear="none">> Thanks,<br clear="none">><br clear="none">> -Michiel</div><br clear="none">><br clear="none">> _______________________________________________<br clear="none">> Biopython mailing list - <a shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none">> <a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><div class="yqt1271370800" id="yqtfd95705"><br clear="none"></div></div><br><br></div> </div> </div> </div></div></body></html>