Skip to content
Snippets Groups Projects
Commit 0d21c643 authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

[ENSCORESW-634]. Memory efficient version for writing EMBL format files.

Slice sequence is written into chunks (as specified by the chunk_factor
parameter given to the constructor) in method write_embl_seq, which now
returns the base counts.
Methods dump_embl has been modified accordingly. A template for a sequence
header is written, then the sequence, then we seek backwards to the
position of the sequence header to write it with the actual base counts
which have been figured out during the writing of the sequence.

Pros: memory efficiency
Cons: cannot dump to a file for which a compressed fh has been obtained,
      i.e. cannot call dump_embl method in a callback provided to
      Bio::EnsEMBL::Utils::IO::gz_work_with_file.
parent a16323f7
No related branches found
No related tags found
No related merge requests found
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment