[Biopython] Increase line length when writing EMBL format

[Peter Cock]

Hello Pedro,

Sadly this annotation value is one of those awkward cases of a long
value with no spaces, so there is no good place to break it for line
wrapping.

Where is your original file from? The input line was 81 characters
long, which I believe is too long.  It is from EMBL themselves? If so,
perhaps we need to more closely match how they now handle this corner
case - which may have changed since I last looked at this code.

Peter

On Fri, Sep 18, 2020 at 1:36 PM Pedro Almeida <p.almeida.mc at gmail.com> wrote:
>
> Dear BioPython Developers and enthusiasts,
>
> I’m working in a script to perform some modifications in an EMBL file format I have at hand. Everything seems to be working OK, except for some features where `SeqIO.write(record, fh, 'embl')` seems to be writing the last closing quote (`"`) in a new line as a feat of its own.
>
> Here’s how the original feature is:
>
> ```
> FT                   /standard_name="species:rnd-4_family-1331|genus:Unspecified"
> ```
>
> but with  `SeqIO.write` gets printed in 2 lines as:
>
> ```
> FT                   /standard_name="species:rnd-4_family-1331|genus:Unspecified
> FT                   "
> ```
>
> I remember seeing (can’t remember where though) that the ‘embl’ format uses for the most part the genbank structure, so thought that increasing the value of `record.GB_LINE_LENGTH` say to 100 `record.GB_LINE_LENGTH=100` could work, but it doesn’t…
>
> I actually think that `record.GB_LINE_LENGTH` is not taken into account with ‘embl’ writing format because the default value seems to be [79](https://biopython.org/docs/1.75/api/Bio.GenBank.Record.html#Bio.GenBank.Record.Record.GB_LINE_LENGTH) but by default it prints the line above with a width of 81.
>
> Any ideas/suggestions on how to work around this? I could probably write another parser to correct for this but would be easier/better if this could be worked with BioPython.
>
> Many thanks,
> Pedro
>
>
>
>
>
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