Generic

Function: paraSync 1.0paraSync - uses paraFetch to recursively mirror url to given path

Usage: paraSync {options} N R URL outPath

Function: Convert ESTs so that orientation matches directory of transcription

Usage: estOrient [options] db estTable outPsl

Function: Generate .ra format from lines with pipe-separated fields

Usage: linesToRa in.txt out.ra

Function: Split text input into files named by column value

Usage: splitFileByColumn source outDir

Function: Sum columns in a text file.

Usage: addCols <fileName>

Function: makeTableList - create/recreate tableList tables (cache of SHOW TABLES)

Usage: makeTableList [assemblies]

Function: Convert fa file to tab separated file

Usage: faToTab infileName outFileName

Function: Convert target coverage of net to a bed file.

Usage: netToBed in.net out.bed

Function: Check to see if a twobit file has any identical sequences in it

Usage: twoBitDup file.2bit

Function: Check for biggest gap in coverage for a list of tracks.For most tracks coverage of 10,000,000 or more will indicate that there wasa mistake in generating the track.

Usage: checkCoverageGaps database track1 ... trackN

Function: Correlate tables via bitmap projections.

Usage: featureBits database table(s)

Function: Make binary version of chromGraph.

Usage: chromGraphToBin in.tab out.chromGraph

Function: Find specified motif in sequence

Usage: findMotif [options] -motif=<acgt...> sequence

Function: Filter out psl file

Usage: pslFilter in.psl out.psl

Function: Select records from a PSL file.

Usage: pslSelect [options] inPsl outPsl