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sum_vals
Martin Asser Hansen edited this page Oct 2, 2015
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sum_vals calculates the total sums for all values of given keys outputting a
record with keys of the type <key>_SUM with the sum as values.
... | sum_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 sum 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 obtain a sum of the second column, read in the table with read_tab and then pipe to sum_vals:
read_tab -i test.tab | sum_vals -k V1 -x
V1_SUM: 174
REC_TYPE: SUM
---
And for two columns:
read_tab -i test.tab | sum_vals -k V1,V2 -x
V1_SUM: 174
REC_TYPE: SUM
V2_SUM: 164
---
To sum the ; seperated values of a given key use the -l switch:
read_tab -i test.tab | sum_vals -l V3
V3_SUM: 15.00
V3: 0;1;2;3;4;5
V0: Human
V2: 78
V1: 123
---
V3_SUM: 21.00
V3: 6;7;8
V0: Dog
V2: 81
V1: 45
---
V3_SUM: 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
sum_vals is part of the Biopieces framework.