[Bioperl-l] fasta format

Jonas Schaer Jonas_Schaer at gmx.de
Tue Dec 8 10:21:58 EST 2009

Hi there,
I have a little question concerning bioperl. I have BioPerl-1.6.1.tar.gz installed and i use the fasta.pm module to read in some fasta files. first it worked fine, but now i have some fastafiles in slightly different format (not all lines have the same length!).

------------- EXCEPTION -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #49 '
..' is 28 != 101 chars.
STACK Bio::DB::Fasta::calculate_offsets C:/Perl/site/lib/Bio/DB/Fasta.pm:771
STACK Bio::DB::Fasta::index_file C:/Perl/site/lib/Bio/DB/Fasta.pm:681
STACK Bio::DB::Fasta::new C:/Perl/site/lib/Bio/DB/Fasta.pm:491
STACK Bio::DB::Fasta::newFh C:/Perl/site/lib/Bio/DB/Fasta.pm:513
STACK main::readfasta blast_eval.pm:174
STACK toplevel blast_eval.pm:83

indexing was interrupted, so unlinking test.fasta.index at C:/Perl/site/lib/Bio/
DB/Fasta.pm line 1054.

Is there any way to use these fasta files with diffrent length of lines with this fasta.pm module or will i have to change the format of my fasta-files(big databases...) ?

Thanks in advance for any help! 

Regards, Jonas

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