Difference between revisions of "Shore sort"

Latest revision as of 10:08, 28 September 2011

shore sort sorts, merges or queries tab-delimited text files.

Usage: shore sort [OPTIONS] [TEXT_FILES]

Allowed options
-i, --infiles=<arg[,...]>		A comma-separated list of plain-text input files
-o, --outfile=<arg>	(Default: stdout)	Output file
-p, --preset=<arg>		Automatically select sort keys for the file type specified. Supported values: * maplist: map.list format sorted by genomic coordinate * maplist_id: map.list format sorted by read ID * reads0: reads flat file format sorted by read ID * gff: GFF format sorted by position
-k, --keystring=<arg>		Concatenation of column ids (counted from 1) and key types. Valid key types: t (text), i (integer) and f (float); capital letters reverse the sort order - e.g. '-k 1i5t3i7I'.
-I, --inplace		Output file is the same as the input file
-t, --tmpdir=<arg>		Temporary file directory (defaults to $TMPDIR or /tmp)
-B, --blocksize=<arg>	(Default: 2048)	Block size in megabytes
-m, --nur-merge		Merge already sorted files
-u, --unique		Output only the first of an equal run
-c, --check		Only test if the files are sorted
-b, --upper-bound=<arg[,...]>		Returns byte offset (counted from 0) and text of the first line in a sorted file that compares greater than the keys given in <arg> (provide comma-separated values in order of key priority)
-T, --tail=<arg[,...]>		Print all lines in a sorted file that compare greater than the keys given in <arg> (provide comma-separated values in order of key priority)
-C, --no-comments		Do not treat line comments and empty lines specially
-v, --verbose		Be more verbose

@@ Line 1: / Line 1: @@
 '''shore sort''' sorts, merges or queries tab-delimited text files.
+==Command line options==
 '''Usage:''' shore sort [OPTIONS] [TEXT_FILES]