Little Tools: Difference between revisions

From genomewiki
Jump to navigationJump to search
No edit summary
No edit summary
Line 10: Line 10:
; [[bedInverseExons]] Inverses exon numbering (python)
; [[bedInverseExons]] Inverses exon numbering (python)
; [[bedFrag]] extract part of bed, pretty dumb (awk)
; [[bedFrag]] extract part of bed, pretty dumb (awk)
; [[bedOverlapName]] add overlapping bedname from second bed (one-line bash)


[[Category:User Developed Scripts]]
[[Category:User Developed Scripts]]

Revision as of 13:11, 29 September 2006

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. I'm trying to add one per week. Please add comments here if you think that something can be done easier with a tool from the source tree.

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)