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

Xu, Lizhe - APHIS Lizhe.Xu at aphis.usda.gov
Fri Jan 6 11:42:16 EST 2012


Thanks Kevin, I installed the package Spreadsheet::ParseExcel but got new error by running the script.



BioPerl 1.6.1 on XP



Script:

#!C:\Perl\bin -w

use Bio::Seq;

use Bio::SeqIO;



$file="PTV1Primers.xls";



$seqio_obj = Bio::SeqIO->new(-file => $file, -format => 'excel' );





while ($seq_obj = $seqio_obj->next_seq){



    print $seq_obj->seq,"\n";



}

......

Error message:
=========================================================
Replacement list is longer than search list at C:/Perl/site/lib/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at C:/Perl/site/lib/Bio/Tree/TreeFunctionsI.pm line 94

Use of uninitialized value $slot in string eq at C:/Perl/site/lib/Bio/Seq/SeqBuilder.pm line 278.
Use of uninitialized value $slot in substr at C:/Perl/site/lib/Bio/Seq/SeqBuilder.pm line 283.
Use of uninitialized value $slot in concatenation (.) or string at C:/Perl/site/lib/Bio/Seq/SeqBuilder.pm line 283.
Use of uninitialized value in print at ReadExcel.pl line 15.
==========================================================

The first two row only displayed when I run the script under Perl v5.12.2. The rest showed on both Perl v5.12.2 and v5.8.8 (different machines) and repeated many times, I guess as many as the row numbers in Excel file.

Please help me to fix the problem or point me a better way to read an excel file with two columns: one for name and one for sequence. Thank you very much.



Lizhe



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