[Genome] is there a fast BED2seq tool?

[Hiram Clawson]

Good Morning Stein:

It has been pointed out to me that there is a command in
the kent source tree which can reverse complement sequence: faRc

> faRc - Reverse complement a FA file
> usage:
>    faRc in.fa out.fa
> In.fa and out.fa may be the same file.
> options:
>    -keepName - keep name identical (don't prepend RC)
>    -keepCase - works well for ACGTUN in either case. bizarre for other 
> letters.
>                without it bases are turned to lower, all else to n's
>    -justReverse - prepends R unless asked to keep name
>    -justComplement - prepends C unless asked to keep name
>                      (cannot appear together with -justReverse)

On 2006 Nov 22, , at 7:56 AM, Hiram Clawson wrote:

> Good Morning Stein:
>
> Surprisingly enough, I do not see a stand alone tool in the source
> tree to do a reverse complement.  There is a function for it of course
> in the libraries, but no command line access to it.
>
> Good idea for such a feature in twoBitToFa.
>
> --Hiram
>
> On 2006 Nov 22, , at 12:12 AM, Stein Aerts wrote:
>
>> Hi Rachel, Hiram,
>>
>> Thanks, this all works very well.
>> I'm left with one detail however: the strand in the BED file is not
>> taken into account when using this:
>>
>> awk '{printf "%s:%d-%d\n", $1, $2, $3}' file.bed \
>>        | twoBitToFa hg18.2bit output.fa -seqList=stdin
>>
>>
>> So I presume it returns only + strand sequences. I could reverse
>> complement the - strand features using a bioperl script, but perhaps
>> it's possible with the ucsc tools in one go?
>>
>> Stein