Howdy, Amit,
For my personal use, I have always used faToTwobit to create 2bit files.
I wrote most of the original seq module in bx-python (circa 2005?), adapting it
from a nib format reader that James Taylor wrote. The main goal at the time
was to read DNA from a variety of sequence file formats. Writing wasn't
considered, since at the time I had no need to write such files.
I'm pretty sure there have been improvements made, but if writing has been
added, I expect it would be supported in lib/bx/seq/seq.py . But I see no
write support there, so I think it has never been added.
It wouldn't take much to write 2bit in python. Format spec is here:
http://genome.ucsc.edu/FAQ/FAQformat#format7
Bob H
On Feb 2, 2012, at 6:30 PM, Amit Indap wrote:
> Hi,
>
> I had a question about the bx python API. I'm using its twobit API to
> read sequence intervals from a two bit file.
> If I had sequence I wanted to write to a 2bit file, is there a way to
> do that with bx-python API? Otherwise, I was going to use FaToTwoBit
> program from jksrc,
> but it would be nice if there is a way I can do it from python.
>
> Thanks for the help!
>
> Amit
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