[Bioperl-l] Error Message
Dibakar Ray
dibakar@hub.nic.in
Mon, 24 Jun 2002 15:37:40 +0530
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I am very new to the world of BioPerl. I am facing few problems. Hope =
'gurus' can help me.
My platform is Linux 6.2
I have installed bioperl bioperl-1.0.1=20
I was trying to run the first example shown in the tutorial at =
http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/1ere_journee=
.html.=20
The code is given below -
use Bio::SeqIO;
my $in =3D Bio::SeqIO->newFh ( -file =3D> '<seqs.sp',
-format =3D> 'swiss' );
my $out =3D Bio::SeqIO->newFh ( -file =3D> '>seqs.fasta',
-format =3D> 'fasta' );
print $out $_ while <$in>;
When I try to run it it gives an Error=20
-------------------EXCEPTION-------------------------------
MSG: swissprot stream with no ID. Not swissprot in my book
STACK Bio::SeqIO::swiss::next_seq =
/usr/lib/perl5/site_perl/5.005/Bio/SeqIO/Swiss.pm:155
STACK Bio::SeqIO::READLINE =
/usr/lib/perl5/site_perl/5.005/Bio/SeqIO.pm:596
STACK toplevel test3.pl:15
-------------------------------------------------------------------------=
------------------------
So I am struc at the very begining. Looking for some help.
Regards
ray
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<META content=3D"MSHTML 5.00.2722.1300" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>I am very new to the world of BioPerl. =
I am facing=20
few problems. Hope 'gurus' can help me.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2>My platform is Linux 6.2</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I have installed bioperl =
<I>bioperl-1.0.1</I> <BR>I=20
was trying to run the first example shown in the tutorial at <A=20
href=3D"http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/1ere=
_journee.html">http://www.pasteur.fr/recherche/unites/sis/formation/biope=
rl/1ere_journee.html</A>.=20
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>The code is given below -</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><BR>use <FONT=20
color=3D#4169e1>Bio::SeqIO</FONT>;<BR><BR><FONT =
color=3D#4169e1>my</FONT> $in =20
=3D Bio::SeqIO->newFh ( -file =3D> <FONT=20
color=3D#228b22>'<seqs.sp'</FONT>,<BR> &n=
bsp; &nb=
sp; =20
-format =3D> <FONT color=3D#228b22>'swiss'</FONT> );<BR><BR><FONT=20
color=3D#4169e1>my</FONT> $out =3D Bio::SeqIO->newFh ( =
-file =3D>=20
<FONT=20
color=3D#228b22>'>seqs.fasta'</FONT>,<BR>  =
; =
=
-format =3D> <FONT color=3D#228b22>'fasta'</FONT> );<BR><BR><BR>print =
$out=20
$_<FONT color=3D#4169e1> while</FONT> <$in>;<BR></FONT></DIV>
<DIV><FONT face=3DArial size=3D2>When I try to run it it gives an Error=20
</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>-------------------EXCEPTION-------------------------------</FON=
T></DIV>
<DIV><FONT face=3DArial size=3D2>MSG: swissprot stream with no ID. Not =
swissprot in=20
my book</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>STACK Bio::SeqIO::swiss::next_seq=20
/usr/lib/perl5/site_perl/5.005/Bio/SeqIO/Swiss.pm:155</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>STACK Bio::SeqIO::READLINE=20
/usr/lib/perl5/site_perl/5.005/Bio/SeqIO.pm:596</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>STACK toplevel test3.pl:15</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------------------------------------------=
---------------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>So I am struc at the very begining. =
Looking for=20
some help.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Regards</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>ray</DIV></FONT></BODY></HTML>
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