<div dir="ltr">Hello,<div><br></div><div>Does BioPerl provide a method for calculated sequence identity or does that only exist via external programs, such as Blast+?  I followed along with the AlignIO_and_SimpleAlign HowTo, but <span style="color:inherit;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:inherit;white-space:pre-wrap;background-color:transparent">Bio::Tools::Run::StandAloneBlast is failing to build </span></div><div><span style="color:inherit;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:inherit;white-space:pre-wrap;background-color:transparent">...</span></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">------------- EXCEPTION -------------</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">MSG: Unknown version output: blastdbcmd: 2.7.1+</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"> Package: blast 2.7.1, build Oct 18 2017 20:40:57</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">....</span></p></div><div><span style="color:inherit;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:inherit;white-space:pre-wrap;background-color:transparent"><br></span></div><div><font face="Menlo, Monaco, Consolas, Courier New, monospace"><span style="white-space:pre-wrap">which is a little frustrating.  A nice slow method would be just fine for a proof of principle for now, but I can't find one.</span></font></div><div><br></div><div>Below is a little script displaying my dream (it uses a DBIx::Class database I wrote that has a bunch around 80K sequences that I'd like to play with using BioPerl). Any advice is appreciated. My apologies if I failed to find something obvious in the docs or how tos! </div><div><br></div><div>Thanks,</div><div>Demian</div><div><span style="color:inherit;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:inherit;white-space:pre-wrap;background-color:transparent"><br></span></div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">use </span><span style="font-variant-ligatures:no-common-ligatures">Modern::Perl;</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(205,121,35)"><span style="font-variant-ligatures:no-common-ligatures">use lib</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'lib'</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">;</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">use </span><span style="font-variant-ligatures:no-common-ligatures">CysDB::Schema;</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">use </span><span style="font-variant-ligatures:no-common-ligatures">Bio::Seq;</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">use </span><span style="font-variant-ligatures:no-common-ligatures">Data::Dumper;</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">my</span><span style="font-variant-ligatures:no-common-ligatures"> </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">$schema</span><span style="font-variant-ligatures:no-common-ligatures"> = CysDB::Schema-></span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">connect</span><span style="font-variant-ligatures:no-common-ligatures">(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'dbi:SQLite:cys.db'</span><span style="font-variant-ligatures:no-common-ligatures">);</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(51,187,200)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">my</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="font-variant-ligatures:no-common-ligatures">$chain1</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> = </span><span style="font-variant-ligatures:no-common-ligatures">$schema->resultset</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'ChainCys'</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">)->find({</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">id</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> => </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">1</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">} );</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(51,187,200)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">my</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="font-variant-ligatures:no-common-ligatures">$chain3</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> = </span><span style="font-variant-ligatures:no-common-ligatures">$schema->resultset</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'ChainCys'</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">)->find({</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">id</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> => </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">3</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">} );</span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><br><span style="font-variant-ligatures:no-common-ligatures"></span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">my</span><span style="font-variant-ligatures:no-common-ligatures"> </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">$seq1</span><span style="font-variant-ligatures:no-common-ligatures"> = Bio::Seq->new(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">-seq</span><span style="font-variant-ligatures:no-common-ligatures"> => </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">$chain1->sequence</span><span style="font-variant-ligatures:no-common-ligatures">, </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">-alphabet</span><span style="font-variant-ligatures:no-common-ligatures"> => </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'protein'</span><span style="font-variant-ligatures:no-common-ligatures">);</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">my</span><span style="font-variant-ligatures:no-common-ligatures"> </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">$seq3</span><span style="font-variant-ligatures:no-common-ligatures"> = Bio::Seq->new(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">-seq</span><span style="font-variant-ligatures:no-common-ligatures"> => </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">$chain3->sequence</span><span style="font-variant-ligatures:no-common-ligatures">, </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">-alphabet</span><span style="font-variant-ligatures:no-common-ligatures"> => </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'protein'</span><span style="font-variant-ligatures:no-common-ligatures">);</span><br></p><div><br></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(82,48,225)"><span style="font-variant-ligatures:no-common-ligatures">#my dream</span></p></div><div><br></div><div>say some_align_function_returning_alignobject($seq1,$seq3)->percent_identity</div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(82,48,225)"><span style="font-variant-ligatures:no-common-ligatures"># Problem area comment</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(82,48,225)">#use  Bio::Tools::Run::StandAloneBlast;</p><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(82,48,225)"><span style="font-variant-ligatures:no-common-ligatures">#$factory = Bio::Tools::Run::StandAloneBlast->new(-outfile => 'bl2seq.out');</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(82,48,225)"><span style="font-variant-ligatures:no-common-ligatures">#my $bl2seq_report = $factory->bl2seq($seq1, $seq2)</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(82,48,225)"><span style="font-variant-ligatures:no-common-ligatures">#print Dumper $bl2seq;</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p></div><div> </div></div>