median_vals
median_vals find the median values for given keys outputting a
record with keys of the type <key>_MEDIAN with the median as values.
Finding the median of a given key involves sorting of all records based
on that key which may cause problems for large datasets.
Consult Wikipedia to learn more about medians:
http://en.wikipedia.org/wiki/Median
... | median_vals [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-k <list> | --keys=<list>] # Comma separated list of keys.
[-l <string> | --list=<string>] # Key with ; separated values to calculate media from.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following table in the file test.tab:
Human 123 78 0;1;2;3;4;5
Dog 45 81 6;7;8
Mouse 6 5 9
To find the median value in the second column, read in the table with read_tab and then pipe to median_vals:
read_tab -i test.tab | median_vals -k V1 -x
V1_MEDIAN: 45
REC_TYPE: MEDIAN
---
For two columns:
read_tab -i test.tab | median_vals -k V1,V2 -x
V1_MEDIAN: 45
REC_TYPE: MEDIAN
V2_MEDIAN: 78
---
Or to get the median for a list of ; separeted values for a specified key
use the -l switch:
read_tab -i test.tab | median_vals -l V3
V3_MEDIAN: 3.50
V3: 0;1;2;3;4;5
V0: Human
V2: 78
V1: 123
---
V3_MEDIAN: 7.00
V3: 6;7;8
V0: Dog
V2: 81
V1: 45
---
V3_MEDIAN: 9.00
V3: 9
V0: Mouse
V2: 5
V1: 6
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
median_vals is part of the Biopieces framework.