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GREPPOS

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

greppos - extract certain positions from sequences.

 

SYNOPSIS

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

 

DESCRIPTION

greppos extracts specified positions from sequences. They are specified in a file with the --file option or by the --range option. They are alignment positions for alignments, otherwise sequence positions. Input is either from file or stdin. The output is sent to stdout.

 

OPTIONS

greppos accepts the following options.

-rrange
--range=range
Extracts the entries specified in range. They are specified as numbers, 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, 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 position numbers 1-20 and 27 from file foo.col:

greppos -r1-20,27 foo.col

Extract entries specified in rangefile from foo.col:

greppos --file rangefile foo.col

rangefile could look like this:


  1,2,3
  6-17

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

greppos --file --sorted rangefile foo.col

 

BUGS

Report 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