[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1099 (fwd)
Jason Stajich
jason@cgt.mc.duke.edu
Fri, 22 Feb 2002 08:26:37 -0500 (EST)
You are not using the Bio::SeqIO module correctly. Please read the
documentation about Bio::SeqIO available in the POD (at
http://docs.bioperl.org or on your machine - % perldoc Bio::SeqIO).
Additionally the bioperl tutorial will help you as well - available linked
from our website.
Bio::SeqIO is a stream of data - not a single sequence. Your code is
corrected below with >>>> in front of lines that have been changed or
added.
use Bio::SeqIO;
$in = Bio::SeqIO->new ('-file' => "test.txt",
'-format' => "Fasta");
require Bio::Tools::RestrictionEnzyme;
$re1 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRI');
>>>>>>>>>>>>my $seq = $in->next_seq
>>>>>>>>>>>>$locations = $re1->cut_locations($seq);
$first = ${$locations}[1];
print " the first location is $first";
-jason
--
Jason Stajich
Duke University
jason@cgt.mc.duke.edu
---------- Forwarded message ----------
Date: Fri, 22 Feb 2002 00:17:03 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1099
JitterBug notification
new message incoming/1099
Message summary for PR#1099
From: Guojun Yang <guojun@idmb.tamu.edu>
Subject: Is this a bug?
Date: Thu, 21 Feb 2002 23:22:39 -0600
0 replies 0 followups
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From: Guojun Yang <guojun@idmb.tamu.edu>
To: "'bioperl-bugs@bio.perl.org'" <bioperl-bugs@bio.perl.org>
Subject: Is this a bug?
Date: Thu, 21 Feb 2002 23:22:39 -0600
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Dear Bioperl,
Thank you for maintain the bipperl, I tried to write a short script to get
the locaiton of enzymatic cuts, it gave me information like this:
Can't locate object method "seq" via package "Bio::SeqIO::fasta" (perhaps
you fo
rgot to load "Bio::SeqIO::fasta"?) at
C:/Perl/site/lib/Bio/Tools/RestrictionEnzy
me.pm line 670.
my script is:
use Bio::SeqIO;
$in = Bio::SeqIO->new ('-file' => "test.txt",
'-format' => "Fasta");
require Bio::Tools::RestrictionEnzyme;
$re1 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRI');
$locations = $re1->cut_locations($in);
$first = ${$locations}[1];
print " the first location is $first";
Is it becaused of a bug in .../RestrictionEnzyme.pm? I am using a Windows
2000 OS? Or could you give me a hint on how to do it?
Thank you very much,
Guojun
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<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
5.5.2654.45">
<TITLE>Is this a bug?</TITLE>
</HEAD>
<BODY>
<P><FONT SIZE=3D2 FACE=3D"Arial">Dear Bioperl,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Thank you for maintain the bipperl, I =
tried to write a short script to get the locaiton of enzymatic cuts, it =
gave me information like this:</FONT></P>
<P><FONT SIZE=3D2 FACE=3D"Arial">Can't locate object method =
"seq" via package "Bio::SeqIO::fasta" (perhaps you =
fo</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">rgot to load =
"Bio::SeqIO::fasta"?) at =
C:/Perl/site/lib/Bio/Tools/RestrictionEnzy</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">me.pm line 670.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">my script is:</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">use Bio::SeqIO;</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">$in =3D Bio::SeqIO->new ('-file' =
=3D> "test.txt",</FONT>
<BR> =
=
<FONT SIZE=3D2 =
FACE=3D"Arial">'-format' =3D> "Fasta");</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">require =
Bio::Tools::RestrictionEnzyme;</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">$re1 =3D new =
Bio::Tools::RestrictionEnzyme(-NAME =3D>'EcoRI');</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">$locations =3D =
$re1->cut_locations($in);</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">$first =3D ${$locations}[1];</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">print " the first location is =
$first";</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">Is it becaused of a bug in =
.../RestrictionEnzyme.pm? I am using a Windows 2000 OS? Or could you =
give me a hint on how to do it?</FONT></P>
<P><FONT SIZE=3D2 FACE=3D"Arial">Thank you very much,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Guojun</FONT>
</P>
</BODY>
</HTML>
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