Each line of the file must be less than 65,536 characters

[Juke34]

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the file must be less than 65,536 characters.
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447
STACK: Bio::DB::IndexedBase::_check_linelength /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757
STACK: Bio::DB::Fasta::_calculate_offsets /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/Fasta.pm:227
STACK: Bio::DB::IndexedBase::_index_files /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:659
STACK: Bio::DB::IndexedBase::index_file /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:487
STACK: Bio::DB::IndexedBase::new /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:364
-------------

Someone knows why there is this limitation? Could we add a patch to fix the sequence to make it shorter in such case?

[hyphaltip]

It’s a limitation in the indexing integer size I believe. Is there a reason you can’t use multi line fasta seqs for this specific challenge. I generally use hmmer esl-sfetch, blast indexes, or cdbfasta for my indexing and retrieval at this point but I understand the desire For native Perl only solutions. Jason Stajich, PhD jasonstajich.phd@gmail.com

…

On Jul 1, 2020, 4:55 AM -0700, Jacques Dainat ***@***.***>, wrote: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Each line of the file must be less than 65,536 characters. STACK: Error::throw STACK: Bio::Root::Root::throw /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::DB::IndexedBase::_check_linelength /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757 STACK: Bio::DB::Fasta::_calculate_offsets /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/Fasta.pm:227 STACK: Bio::DB::IndexedBase::_index_files /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:659 STACK: Bio::DB::IndexedBase::index_file /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:487 STACK: Bio::DB::IndexedBase::new /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:364 Someone knows why there is this limitation? Could we add a parch to fix the sequence to make it shorter in such case? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[Juke34]

I made a toolkit (AGAT) and I have several scripts using Bio::DB::Fasta. Myself I never use single line fasta files, but I got several time user feedbacks having this error. Apparently it is not rare that people use single line fasta files. The fix is always to reformat the file before, but maybe there is an easy way to fix the sequence on the fly (refold it) when calling Bio::DB::Fasta.

[cjfields]

@Juke34 the problem is that the index is built based on the location of the record delimiters in the file.

(to add to @hyphaltip 's alternatives, I've been using samtosls faidx for quite a while).

[cjfields]

@Juke34 BTW I should have mentioned back in August that a patch is more than welcome.

[Juke34]

I don’t see any obvious way to patch that.