Little Tools: Difference between revisions
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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 there is so little documentation | 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) | ; [[bedProject]] Will add or substract numbers from positions in a bed file (gawk) | ||
; [[bedTotalSize]] Prints length of region covered by bedfile (python) | ; [[bedTotalSize]] Prints length of region covered by bedfile (python) | ||
; [[ucsc]] Uploads a file to your favorite ftp server and displays it on the UCSC of your choice (bash) | ; [[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 | |||
[[Category:User Developed Scripts]] | |||
Latest revision as of 13:44, 24 June 2010
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
