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Re: Parsing .2bit DNA filesby bobf (Monsignor) |
on Mar 06, 2008 at 04:08 UTC ( [id://672350]=note: print w/replies, xml ) | Need Help?? |
Nice example++. Thanks for posting the code. The 2bit format is used by the BLAT program for aligning DNA sequences. The BLAT suite of programs contains two utilities that might be of interest:
The twoBitToFa documentation is as follows:
Once the sequence is converted back to fasta format it can be easily manipulated using a variety of tools (Perl, BioPerl, sequence utility programs, etc). So yes, a utility does exist that meets at least some of your listed requirements. OTOH, another tool in the toolbox, especially if it is pure Perl and/or a snazzy wrapper around a command-line utility, is always welcome. :-)
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