Little Tools

This is supposed to become a little collection of tools to facilitate everyday work with the UCSC file formats/tools. It's possible that they already exist somewhere in the the source tree but since I originally had (and there still is) so little documentation for the source tree, I might have overlooked them.

bedProject Will add or substract numbers from positions in a bed file (gawk)

bedTotalSize Prints length of region covered by bedfile (python)

bedRegion Prints the maximum range coverd by a bed (gawk)

ucsc Uploads a file to your favorite ftp server and displays it on the UCSC of your choice with firefox (bash)

log little scripts to keep logfiles of what you are doing, very handy (bash)

bedBlastLift script to lift features from one sequence to another using tblastx (python)

bedFlanking annotate flanking genes to bed file (C, with jklib)

bedInverseExons Inverses exon numbering (python)

bedFrag extract part of bed, pretty dumb (awk)

bedOverlapName add overlapping bedname from second bed (one-line bash)

textReplace translate words in textfiles (python)

bed2UCSC upload a BED file to UCSC wiki track