Simple Sequence alignment, StandAloneBlast build failure, and also seeking advice
Demian Riccardi <[email protected]> Fri, 8 Dec 2017 10:40:41 -0700
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <CACaGo3M5YmZf8Q8RJ-SrEQJBM0T995HDV-8xYwdZaP9JdM_xKA@mail.gmail.com> |
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Hello,
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 Bio::Tools::Run::StandAloneBlast is
failing to build
...
------------- EXCEPTION -------------
MSG: Unknown version output: blastdbcmd: 2.7.1+
Package: blast 2.7.1, build Oct 18 2017 20:40:57
....
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.
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!
Thanks,
Demian
use Modern::Perl;
use lib 'lib';
use CysDB::Schema;
use Bio::Seq;
use Data::Dumper;
my $schema = CysDB::Schema->connect('dbi:SQLite:cys.db');
my $chain1 = $schema->resultset('ChainCys')->find({id => 1} );
my $chain3 = $schema->resultset('ChainCys')->find({id => 3} );
my $seq1 = Bio::Seq->new(-seq => $chain1->sequence, -alphabet => 'protein');
my $seq3 = Bio::Seq->new(-seq => $chain3->sequence, -alphabet => 'protein');
#my dream
say some_align_function_returning_alignobject($seq1,$seq3)->percent_identity
# Problem area comment
#use Bio::Tools::Run::StandAloneBlast;
#$factory = Bio::Tools::Run::StandAloneBlast->new(-outfile => 'bl2seq.out');
#my $bl2seq_report = $factory->bl2seq($seq1, $seq2)
#print Dumper $bl2seq;
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<div dir=3D"ltr">Hello,<div><br></div><div>Does BioPerl provide a method fo=
r calculated sequence identity or does that only exist via external program=
s, such as Blast+?=C2=A0 I followed along with the=C2=A0AlignIO_and_SimpleA=
lign HowTo, but=C2=A0<span style=3D"color:inherit;font-family:Menlo,Monaco,=
Consolas,"Courier New",monospace;font-size:inherit;white-space:pr=
e-wrap;background-color:transparent">Bio::Tools::Run::StandAloneBlast is fa=
iling to build=C2=A0</span></div><div><span style=3D"color:inherit;font-fam=
ily:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:inher=
it;white-space:pre-wrap;background-color:transparent">...</span></div><div>=
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures">------------- EXCEPTION -------------</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures">MSG: Unknown version output: blastdbcmd: 2.7.1+</span=
></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures">=C2=A0Package: blast 2.7.1, build Oct 18 2017 20:40:5=
7</span></p><p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-=
height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-varia=
nt-ligatures:no-common-ligatures">....</span></p></div><div><span style=3D"=
color:inherit;font-family:Menlo,Monaco,Consolas,"Courier New",mon=
ospace;font-size:inherit;white-space:pre-wrap;background-color:transparent"=
><br></span></div><div><font face=3D"Menlo, Monaco, Consolas, Courier New, =
monospace"><span style=3D"white-space:pre-wrap">which is a little frustrati=
ng. 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 wrot=
e that has a bunch around 80K sequences that I'd like to play with usin=
g BioPerl). Any advice is appreciated. My apologies if I failed to find som=
ething obvious in the docs or how tos!=C2=A0</div><div><br></div><div>Thank=
s,</div><div>Demian</div><div><span style=3D"color:inherit;font-family:Menl=
o,Monaco,Consolas,"Courier New",monospace;font-size:inherit;white=
-space:pre-wrap;background-color:transparent"><br></span></div><p style=3D"=
margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-famil=
y:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures:no-common-l=
igatures;color:rgb(205,121,35)">use </span><span style=3D"font-variant-liga=
tures:no-common-ligatures">Modern::Perl;</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(205,121,35)"><span style=3D"font-variant-liga=
tures:no-common-ligatures">use lib</span><span style=3D"font-variant-ligatu=
res:no-common-ligatures;color:rgb(0,0,0)"> </span><span style=3D"font-varia=
nt-ligatures:no-common-ligatures;color:rgb(195,55,32)">'lib'</span>=
<span style=3D"font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"=
>;</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style=3D"font-v=
ariant-ligatures:no-common-ligatures"></span><br></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures;color:rgb(205,121,35)">use </span><span style=3D"font-=
variant-ligatures:no-common-ligatures">CysDB::Schema;</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures;color:rgb(205,121,35)">use </span><span style=3D"font-=
variant-ligatures:no-common-ligatures">Bio::Seq;</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures;color:rgb(205,121,35)">use </span><span style=3D"font-=
variant-ligatures:no-common-ligatures">Data::Dumper;</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style=3D"font-v=
ariant-ligatures:no-common-ligatures"></span><br></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures;color:rgb(205,121,35)">my</span><span style=3D"font-va=
riant-ligatures:no-common-ligatures"> </span><span style=3D"font-variant-li=
gatures:no-common-ligatures;color:rgb(51,187,200)">$schema</span><span styl=
e=3D"font-variant-ligatures:no-common-ligatures"> =3D CysDB::Schema-></s=
pan><span style=3D"font-variant-ligatures:no-common-ligatures;color:rgb(205=
,121,35)">connect</span><span style=3D"font-variant-ligatures:no-common-lig=
atures">(</span><span style=3D"font-variant-ligatures:no-common-ligatures;c=
olor:rgb(195,55,32)">'dbi:SQLite:cys.db'</span><span style=3D"font-=
variant-ligatures:no-common-ligatures">);</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style=3D"font-v=
ariant-ligatures:no-common-ligatures"></span><br></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(51,187,200)"><span style=3D"font-variant-liga=
tures:no-common-ligatures;color:rgb(205,121,35)">my</span><span style=3D"fo=
nt-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span st=
yle=3D"font-variant-ligatures:no-common-ligatures">$chain1</span><span styl=
e=3D"font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> =3D </sp=
an><span style=3D"font-variant-ligatures:no-common-ligatures">$schema->r=
esultset</span><span style=3D"font-variant-ligatures:no-common-ligatures;co=
lor:rgb(0,0,0)">(</span><span style=3D"font-variant-ligatures:no-common-lig=
atures;color:rgb(195,55,32)">'ChainCys'</span><span style=3D"font-v=
ariant-ligatures:no-common-ligatures;color:rgb(0,0,0)">)->find({</span><=
span style=3D"font-variant-ligatures:no-common-ligatures;color:rgb(195,55,3=
2)">id</span><span style=3D"font-variant-ligatures:no-common-ligatures;colo=
r:rgb(0,0,0)"> =3D> </span><span style=3D"font-variant-ligatures:no-comm=
on-ligatures;color:rgb(195,55,32)">1</span><span style=3D"font-variant-liga=
tures:no-common-ligatures;color:rgb(0,0,0)">} );</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(51,187,200)"><span style=3D"font-variant-liga=
tures:no-common-ligatures;color:rgb(205,121,35)">my</span><span style=3D"fo=
nt-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span st=
yle=3D"font-variant-ligatures:no-common-ligatures">$chain3</span><span styl=
e=3D"font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> =3D </sp=
an><span style=3D"font-variant-ligatures:no-common-ligatures">$schema->r=
esultset</span><span style=3D"font-variant-ligatures:no-common-ligatures;co=
lor:rgb(0,0,0)">(</span><span style=3D"font-variant-ligatures:no-common-lig=
atures;color:rgb(195,55,32)">'ChainCys'</span><span style=3D"font-v=
ariant-ligatures:no-common-ligatures;color:rgb(0,0,0)">)->find({</span><=
span style=3D"font-variant-ligatures:no-common-ligatures;color:rgb(195,55,3=
2)">id</span><span style=3D"font-variant-ligatures:no-common-ligatures;colo=
r:rgb(0,0,0)"> =3D> </span><span style=3D"font-variant-ligatures:no-comm=
on-ligatures;color:rgb(195,55,32)">3</span><span style=3D"font-variant-liga=
tures:no-common-ligatures;color:rgb(0,0,0)">} );</span><br></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><br><span style=3D"fo=
nt-variant-ligatures:no-common-ligatures"></span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures;color:rgb(205,121,35)">my</span><span style=3D"font-va=
riant-ligatures:no-common-ligatures"> </span><span style=3D"font-variant-li=
gatures:no-common-ligatures;color:rgb(51,187,200)">$seq1</span><span style=
=3D"font-variant-ligatures:no-common-ligatures"> =3D Bio::Seq->new(</spa=
n><span style=3D"font-variant-ligatures:no-common-ligatures;color:rgb(195,5=
5,32)">-seq</span><span style=3D"font-variant-ligatures:no-common-ligatures=
"> =3D> </span><span style=3D"font-variant-ligatures:no-common-ligatures=
;color:rgb(51,187,200)">$chain1->sequence</span><span style=3D"font-vari=
ant-ligatures:no-common-ligatures">, </span><span style=3D"font-variant-lig=
atures:no-common-ligatures;color:rgb(195,55,32)">-alphabet</span><span styl=
e=3D"font-variant-ligatures:no-common-ligatures"> =3D> </span><span styl=
e=3D"font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'=
protein'</span><span style=3D"font-variant-ligatures:no-common-ligature=
s">);</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0)"><span style=3D"font-variant-ligatures=
:no-common-ligatures;color:rgb(205,121,35)">my</span><span style=3D"font-va=
riant-ligatures:no-common-ligatures"> </span><span style=3D"font-variant-li=
gatures:no-common-ligatures;color:rgb(51,187,200)">$seq3</span><span style=
=3D"font-variant-ligatures:no-common-ligatures"> =3D Bio::Seq->new(</spa=
n><span style=3D"font-variant-ligatures:no-common-ligatures;color:rgb(195,5=
5,32)">-seq</span><span style=3D"font-variant-ligatures:no-common-ligatures=
"> =3D> </span><span style=3D"font-variant-ligatures:no-common-ligatures=
;color:rgb(51,187,200)">$chain3->sequence</span><span style=3D"font-vari=
ant-ligatures:no-common-ligatures">, </span><span style=3D"font-variant-lig=
atures:no-common-ligatures;color:rgb(195,55,32)">-alphabet</span><span styl=
e=3D"font-variant-ligatures:no-common-ligatures"> =3D> </span><span styl=
e=3D"font-variant-ligatures:no-common-ligatures;color:rgb(195,55,32)">'=
protein'</span><span style=3D"font-variant-ligatures:no-common-ligature=
s">);</span><br></p><div><br></div><div><p style=3D"margin:0px;font-stretch=
:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(82,48=
,225)"><span style=3D"font-variant-ligatures:no-common-ligatures">#my dream=
</span></p></div><div><br></div><div>say some_align_function_returning_alig=
nobject($seq1,$seq3)->percent_identity</div><div><p style=3D"margin:0px;=
font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;col=
or:rgb(0,0,0);min-height:13px"><span style=3D"font-variant-ligatures:no-com=
mon-ligatures"></span><br></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(82,48,225)"><span style=3D"font-variant-ligat=
ures:no-common-ligatures"># Problem area comment</span></p><p style=3D"marg=
in:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Me=
nlo;color:rgb(82,48,225)">#use=C2=A0 Bio::Tools::Run::StandAloneBlast;</p><=
div><span style=3D"font-variant-ligatures:no-common-ligatures"><br></span><=
/div><p style=3D"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=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(82,48,225)"><span style=3D"font-variant-ligat=
ures:no-common-ligatures">#$factory =3D Bio::Tools::Run::StandAloneBlast-&g=
t;new(-outfile =3D> 'bl2seq.out');</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style=3D"font-v=
ariant-ligatures:no-common-ligatures"></span><br></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(82,48,225)"><span style=3D"font-variant-ligat=
ures:no-common-ligatures">#my $bl2seq_report =3D $factory->bl2seq($seq1,=
$seq2)</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style=3D"font-v=
ariant-ligatures:no-common-ligatures"></span><br></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(82,48,225)"><span style=3D"font-variant-ligat=
ures:no-common-ligatures">#print Dumper $bl2seq;</span></p>
<p style=3D"margin:0px;font-stretch:normal;font-size:11px;line-height:norma=
l;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style=3D"font-v=
ariant-ligatures:no-common-ligatures"></span><br></p></div><div>=C2=A0</div=
></div>
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