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Question: Bx.Seq.Twobit - Write A 2Bit File?
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gravatar for Amit Indap
6.8 years ago by
Amit Indap • 60
Amit Indap • 60 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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modified 6.8 years ago by Bob Harris • 190 • written 6.8 years ago by Amit Indap • 60
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gravatar for Bob Harris
6.8 years ago by
Bob Harris • 190
United States
Bob Harris • 190 wrote:
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
ADD COMMENT • link written 6.8 years ago by Bob Harris • 190
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