Little Tools: Difference between revisions
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; [[log]] little scripts to keep logfiles of what you are doing, very handy (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) | ; [[bedBlastLift]] script to lift features from one sequence to another using tblastx (python) | ||
; [[bedFlanking]] annotate flanking genes to bed file (C, with jklib) | |||
[[Category:User Developed Scripts]] | [[Category:User Developed Scripts]] | ||
Revision as of 13:46, 12 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)
