These utilities can probably already do what you want:
Available for 64-bit download here:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
(you can also download the source and compile, see the FAQs)
[hgwdev:lib> twoBitToFa
twoBitToFa - Convert all or part of .2bit file to fasta
usage:
twoBitToFa input.2bit output.fa
options:
-seq=name - restrict this to just one sequence
-start=X - start at given position in sequence (zero-based)
-end=X - end at given position in sequence (non-inclusive)
-seqList=file - file containing list of the desired sequence names
in the format seqSpec[:start-end], e.g. chr1 or
chr1:0-189
where coordinates are half-open zero-based, i.e.
[start,end)
-noMask - convert sequence to all upper case
-bpt=index.bpt - use bpt index instead of built in one
-bed=input.bed - grab sequences specified by input.bed. Will exclude
introns
Sequence and range may also be specified as part of the input
file name using the syntax:
/path/input.2bit:name
or
/path/input.2bit:name
or
/path/input.2bit:name:start-end
[hgwdev:lib> twoBitInfo
twoBitInfo - get information about sequences in a .2bit file
usage:
twoBitInfo input.2bit output.tab
options:
-nBed instead of seq sizes, output BED records that define
areas with N's in sequence
-noNs outputs the length of each sequence, but does not count Ns
Output file has the columns::
seqName size
The 2bit file may be specified in the form path:seq or
path:seq1,seq2,seqN...
so that information is returned only on the requested sequence(s).
If the form path:seq:start-end is used, start-end is ignored.
-Galt
8/4/2011 11:44 AM, Jens Lichtenberg:
> Hello,
>
> I am would like to use the logic outlined in the genome browser source code
> for twoBit.h in another tool I am working on. Is it at all possible to use
> the components of the genome browser in a simple/meaningful way?
>
> In detail I would like to do something like this (extract the characters
> between position 2000 and 3000 of chromosome 1 in a 2bit file):
>
> #include<iostream>
> #include<twoBit.h>
>
> using namespace std;
> using namespace genome_browser; //I am not sure if this at all exists or
> would even make sense in this case
>
> int main (int argc, char *argv[])
> {
> string bit_file = argv[1];
>
> cout<< twoBitReadSeqFrag(bit_file, 1, 2000, 3000);<< endl;
> }
>
> Thank you so much for your help.
>
> Jens
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
