GenBank output mode leaves trailing whitespace that breaks compatiliity with certain tools

[JamieHeather]

I received an issue by email from Gabriel Ouellet Lavallée, regarding the .gb output modes not being compatible with Unipro Ugene:

The .gb file would not open, giving an error for truncated sequence. It was caused by an empty line inserted after the DNA sequence and before the // marking the end of the sequence. The .gb file opens fine when this line is removed with a text editor.

I found where this NCBI formatting is written in stitchrfunctions.py and modified :

" dna_text +=' '.join([num_pad(pos, pad_len)] + line) + '\n' "
to
" dna_text += '\n' + ' '.join([num_pad(pos, pad_len)] + line) "

This way it only creates a new line if there is still sequence to write, not systematically after a line of sequence. There is no more empty line between DNA sequence and //.

It seems the two tools I use to check .gb files (Snapgene and ApE) both tolerate this extra whitespace, so I'd never have caught this error.