[Bioperl-l] Bio::SeqIO::excel

Kevin Brown Kevin.M.Brown at asu.edu
Thu Jan 5 15:20:04 EST 2012


As the error message notes, you are missing a needed module for the
excel parser to work, namely Spreadsheet::ParseExcel

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Xu, Lizhe -
APHIS
Sent: Thursday, January 05, 2012 11:52 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bio::SeqIO::excel


I tried to use Bio::SeqIO to read an Excel file but got some error
message. The following info includes my running env and screenshots.
Please help me to fix the problem. Thank you very much.


  *   The version of Bioperl you're working with.
1.6.1
[cid:image001.png at 01CCCBA0.3DA8CBA0]

  *   The platform or operating system you're using.
Window XP
  *   What you are trying to do.
Read the excel file with two columns (name of primer, primer sequence)
without head row
#!C:\Perl\bin -w
use Bio::Seq;
use Bio::SeqIO;

$file="ViralPrimers.xls";
$seqio_obj = Bio::SeqIO->new(-file => $file, -format => 'excel' );
......
[cid:image002.jpg at 01CCCBA0.3DA8CBA0]

When I added the following statement to the script, use
Bio::SeqIO::excel;

[cid:image003.jpg at 01CCCBA0.3DA8CBA0]


Lizhe Xu, PhD
Microbiologist
PVSS, FADDL, APHIS, USDA
Plum Island Animal Disease Center
Greenport, NY 11944
Tel: 631 323 3023
fax: 631 323 3366
Lizhe.Xu at aphis.usda.gov<mailto:Lizhe.Xu at aphis.usda.gov>




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