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GREPCOL

Section: User Commands (1)
Updated: September 2000
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NAME

grepcol - extract certain entries from col file.

 

SYNOPSIS

grepcol
[-s | --sorted] [-rrange | -range=range | -f | --file] [rangefile] [file]

 

DESCRIPTION

grepcol extracts specified entries from a col file. They are specified in a file with the --file option or by the --range option. They can be given as numbers or entry names. Input is either from file or stdin. The output is sent to stdout.

 

OPTIONS

grepcol accepts the following options.

-rrange
--range=range
Extracts the entries specified in range. They are specified as numbers or entry names, seperated by commas.

-f
--file
Extracts the entries specified in rangefile which should be present as the first file after the command line options. Entries are specified as numbers or entry names, seperated by commas or newlines.

-s
--sorted
Assumes that the specified entries are ordered. This makes the program run faster. When specifying entry names, it is essential that they ar e all present in the col file.

 

EXAMPLES

Extract entries number 1-5 and 7 from file foo.col:

grepcol -r1-5,7 foo.col

Extract entries specified in rangefile from foo.col:

grepcol --file rangefile foo.col

rangefile could look like this:


  1,2,3
  6,7
  tiger,panther
  lion

Extract entries specified in rangefile from foo.col, where the specifications are sorted as in col file:

grepcol --file --sorted rangefile foo.col

 

BUGS

Commas can not be part of entry names, since they are used to seperate entries. Entry names cannot start with a number.

Report other bugs to col-bugs@bioinf.au.dk.

 

AUTHOR

Bjarne Knudsen (bk@daimi.au.dk)

 

SEE ALSO


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
BUGS
AUTHOR
SEE ALSO


Comments, questions, etc., email gorodkin@genome.ku.dk.


Last updated March 26th, 2007 by Jan Gorodkin