[Bioperl-l] a problem when using the Bio::DB::Fasta

[Guifeng Wei]

Hi,

i have revised my scripts according to the previous email from Florent.
However, there were still some errors which frustrated me so much.

The errors are as follows:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #301451 '
..' is 22 != 51 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
STACK: Bio::DB::Fasta::calculate_offsets
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm:770
STACK: Bio::DB::Fasta::index_dir
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm:593
STACK: Bio::DB::Fasta::new
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm:488
STACK: bed2fasta.pl:13
-----------------------------------------------------------
indexing was interrupted, so unlinking
/home/wgf/elegans190.dna//directory.index at
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm line 1053
But in the directory /home/wgf/elegans190.dna/ , it concludes 6 files,
each contains the complete sequences from one single chromosome, the format
is fasta. The extension of the FASTA files is .fa. Every single file is
started as ">chromosoemeXXX" followed by the thousands of sequences.

and therefore, it warn me that "Each line of the fasta entry must be the
same length except the last". and "indexing was interrupted, so unlinking
/home/wgf/elegans190.dna//directory".

i was much confused about this. so for help.

Wei Guifeng