[BioPython] GenBank Parser and large files?

[Peter]

Stephan Herschel wrote:
> Hi Peter,
> 
> Thanks for the the fast solution! (I guessed that I could not be the
> only one having this problem ...)
>
> Apparently I applied the patch successfully - only the 'Reversed
> patch'- message was confusing - as you can see here:

Yeah - that was the first time I ever created a patch file, and in the 
absence of any instructions on the BioPython developers list, I just 
improvised:

diff my_version.py vcs_version.py > patch.txt

Would the reversed patch messages would go away if I had done this?

diff vcs_version.py my_version.py > patch.txt

> (Stripping trailing CRs from patch.)

Those are because I did this on Windows.

> can't find file to patch at input line 1
> 
> Perhaps you should have used the -p or --strip option?

The --strip option doesn't exist on my version of diff, and -p is an 
alias for --show-c-function (Show which C function each change is in) 
which doesn't seem relevant:-

diff (GNU diffutils) 2.8.7
(The cygwin version running on Windows)

> Tested the parser - works just fine!

Great.

Please let me know (or post on the bug) if you have any trouble with the 
patch - or even if it works fine for you.

http://bugzilla.open-bio.org/show_bug.cgi?id=1747

What sort of GenBank files are you using, and where are they from?

I have mainly been using bacteria from the NCBI - watch out for bug 1758 
and bug 1762 as my patch will probably also fail on those.

Peter
-- 
PhD Student
MOAC Doctoral Training Centre
University of Warwick, UK