Hi Michiel, We do not have the source code, either (and we are in the process of changing our programs to use faFrag instead of fasta-subseq to avoid problems should the binary be lost in the future), but the usage statement indicates that it uses 1-based coordinates:
$ ./fasta-subseq -help usage: seqfile lo hi [strand] (1 indexed) If you like, we can send you our binary so that you can test what it does with the Fasta headers. -- Brooke Rhead UCSC Genome Bioinformatics Group On 3/15/12 8:26 PM, Michiel de Hoon wrote: > Dear all, > > I am looking for the source code (or a binary) of the fasta-subseq > program that is used in blastz-run-ucsc to abridge repeat regions. > This previous message on the mailing list: > > https://lists.soe.ucsc.edu/pipermail/genome/2006-June/010902.html > > says that this program was compiled from PSU source code. However, I > couldn't find this program or its source code there. Does anybody > know where to find this program? If not, is its usage described > somewhere in detail? In particular I am wondering if fasta-subseq > uses 1-based coordinates or 0-based coordinates, and if it modifies > the header lines in the Fasta file in some way. > > Thanks, Michiel de Hoon RIKEN Omics Science Center > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
