## table of contents

DATAMASH(1) | User Commands | DATAMASH(1) |

# NAME¶

datamash - command-line calculations# SYNOPSIS¶

**datamash**[

*OPTION*]

*op*[

*fld*] [

*op fld*...]

# DESCRIPTION¶

Performs numeric/string operations on input from stdin.'op' is the operation to perform. If a primary operation is used,
it must be listed first, optionally followed by other operations. 'fld' is
the input field to use. 'fld' can be a number (1=first field), or a field
name when using the **-H** or **--header-in** options. Multiple fields
can be listed with a comma (e.g. 1,6,8). A range of fields can be listed
with a dash (e.g. 2-8). Use colons for operations which require a pair of
fields (e.g. 'pcov 2:6').

## Primary operations:¶

- groupby, crosstab, transpose, reverse, check

## Line-Filtering operations:¶

- rmdup

## Per-Line operations:¶

- base64, debase64, md5, sha1, sha256, sha512, bin, strbin, round, floor, ceil, trunc, frac

## Numeric Grouping operations:¶

- sum, min, max, absmin, absmax, range

## Textual/Numeric Grouping operations:¶

- count, first, last, rand, unique, collapse, countunique

## Statistical Grouping operations:¶

- mean, trimmean, median, q1, q3, iqr, perc, mode, antimode, pstdev, sstdev, pvar, svar, mad, madraw, pskew, sskew, pkurt, skurt, dpo, jarque, scov, pcov, spearson, ppearson

## Grouping Options:¶

**-C**,**--skip-comments**- skip comment lines (starting with '#' or ';' and optional whitespace)
**-f**,**--full**- print entire input line before op results (default: print only the grouped keys)
**-g**,**--group**=*X[*,Y,Z]- group via fields X,[Y,Z]; equivalent to primary operation 'groupby'
**--header-in**- first input line is column headers
**--header-out**- print column headers as first line
**-H**,**--headers**- same as '--header-in
**--header-out**' **-i**,**--ignore-case**- ignore upper/lower case when comparing text; this affects grouping, and string operations
**-s**,**--sort**- sort the input before grouping; this removes the need to manually pipe the input through 'sort'

## File Operation Options:¶

**--no-strict**- allow lines with varying number of fields
**--filler**=*X*- fill missing values with X (default %s)

## General Options:¶

**-t**,**--field-separator**=*X*- use X instead of TAB as field delimiter
**--format**=*FORMAT*- print numeric values with printf style floating-point FORMAT.
**--output-delimiter**=*X*- use X instead as output field delimiter (default: use same delimiter as
**-t**/-W) **--narm**- skip NA/NaN values
**-R**,**--round**=*N*- round numeric output to N decimal places
**-W**,**--whitespace**- use whitespace (one or more spaces and/or tabs) for field delimiters
**-z**,**--zero-terminated**- end lines with 0 byte, not newline
**--help**- display this help and exit
**--version**- output version information and exit

# OPTIONS¶

# AVAILABLE OPERATIONS¶

## Primary Operations¶

Primary operations affect the way the file is processed. If used, the primary operation must be listed first. Some operations require field numbers (groupby, crosstab) while others do not (reverse,check,transpose). If primary operation is not listed the entire file is processed - either line-by-line (for 'per-line' operations) or all lines as one group (for grouping operations). See Examples section below.**groupby X,Y,... op fld ...**- group the file by given fields. Equivalent to option '-g'. For each group
perform operation
**op**on field**fld**. **crosstab X,Y [op fld ...]**- cross-tabulate a file by two fields (cross-tabulation is also known as pivot tables). If no operation is specified, counts how many incidents exist of X,Y.
**transpose**- transpose rows, columns of the input file
**reverse**- reverse field order in each line
**check [N lines] [N fields]**- verify the input file has same number of fields in all lines, or the expected number of lines/fields. number of lines and fields are printed to STDOUT. Exits with non-zero code and prints the offending line if there's a mismatch in the number of lines/ fields.

## Line-Filtering operations¶

**rmdup**- remove lines with duplicated key value

## Per-Line operations¶

**base64**- Encode the field as base64
**debase64**- Decode the field as base64, exit with error if invalid base64 string
**md5/sha1/sha256/sha512**- Calculate md5/sha1/sha256/sha512 hash of the field value
**bin[:BUCKET-SIZE]**- bin numeric values into buckets of size
**BUCKET-SIZE**(defaults to 100). **strbin[:BUCKET-SIZE]**- hashes the input and returns a numeric integer value between zero and
**BUCKET-SIZE****(defaults to 10).** **round/floor/ceil/trunc/frac**- numeric rounding operations. round (round half away from zero), floor (round up), ceil (ceiling, round down), trunc (truncate, round towards zero), frac (fraction, return fraction part of a decimal-point value).

## Numeric Grouping operations¶

**sum**- sum the of values
**min**- minimum value
**max**- maximum value
**absmin**- minimum of the absolute values
**absmax**- maximum of the absolute values
**range**- the values range (max-min)

## Textual/Numeric Grouping operations¶

**count**- count number of elements in the group
**first**- the first value of the group
**last**- the last value of the group
**rand**- one random value from the group
**unique**- comma-separated sorted list of unique values
**collapse**- comma-separated list of all input values
**countunique**- number of unique/distinct values

## Statistical Grouping operations¶

A**p/s**prefix indicates the variant:

**p**opulation or

**s**ample. Typically, the

**s**ample variant is equivalent with

**GNU R**'s internal functions (e.g datamash's

**sstdev**operation is equivalent to R's

**sd()**function).

**mean**- mean of the values
**trimmean[:PERCENT]**- trimmed mean of the values.
**PERCENT**should be between 0 and 0.5. (**trimmean:0**is equivalent to**mean**.**trimmean:0.5**is equivalent to**median**). **median**- median value
**q1**- 1st quartile value
**q3**- 3rd quartile value
**iqr**- inter-quartile range
**perc[:PERCENTILE]**- percentile value
**PERCENTILE**(defaults to 95). **mode**- mode value (most common value)
**antimode**- anti-mode value (least common value)
**pstdev/sstdev**- population/sample standard deviation
**pvar/svar**- population/sample variance
**mad**- median absolute deviation, scaled by constant 1.4826 for normal distributions
**madraw**- median absolute deviation, unscaled
**pskew/sskew**- skewness of the group
values x reported by 'sskew' and 'pskew' operations:
x > 0 - positively skewed / skewed right 0 > x - negatively skewed / skewed left x > 1 - highly skewed right 1 > x > 0.5 - moderately skewed right 0.5 > x > -0.5 - approximately symmetric -0.5 > x > -1 - moderately skewed left -1 > x - highly skewed left

**pkurt/skurt**- excess Kurtosis of the group
**jarque/dpo**- p-value of the Jarque-Beta (
**jarque**) and D'Agostino-Pearson Omnibus (**dpo**) tests for normality: null hypothesis is normality; low p-Values indicate non-normal data; high p-Values indicate null-hypothesis cannot be rejected. **pcov/scov [X:Y]**- covariance of fields X and Y
**ppearson/spearson [X:Y]**- Pearson product-moment correlation coefficient [Pearson's R] of fields X and Y

# EXAMPLES¶

## Basic usage¶

Print the sum and the mean of values from field 1:$ seq 10 |datamashsum 1 mean 1 55 5.5

Group input based on field 1, and sum values (per group) on field 2:

$ cat example.txt A 10 A 5 B 9 B 11 $datamash-g 1 sum 2 < example.txt A 15 B 20 $datamashgroupby 1 sum 2 < example.txt A 15 B 20

Unsorted input must be sorted (with '-s'):

$ cat example.txt A 10 C 4 B 9 C 1 A 5 B 11 $datamash-s -g1 sum 2 < example.txt A 15 B 20 C 5

Which is equivalent to:

$ cat example.txt | sort -k1,1 |datamash-g 1 sum 2

## Header lines¶

Use**-h**

**(--headers)**if the input file has a header line:

# Given a file with student name, field, test score... $ head -n5 scores_h.txt Name Major Score Shawn Engineering 47 Caleb Business 87 Christian Business 88 Derek Arts 60 # Calculate the mean and standard devian for each major $datamash--sort --headers --group 2 mean 3 pstdev 3 < scores_h.txt (or use short form) $datamash-sH -g2 mean 3 pstdev 3 < scores_h.txt (or use named fields) $datamash-sH -g Major mean Score pstdev Score < scores_h.txt GroupBy(Major) mean(Score) pstdev(Score) Arts 68.9 10.1 Business 87.3 4.9 Engineering 66.5 19.1 Health-Medicine 90.6 8.8 Life-Sciences 55.3 19.7 Social-Sciences 60.2 16.6

## Skipping comment lines¶

Use**-C**

**(--skip-comments)**to skip lines starting with ´#´ or ´;´ characters (and optional whitespace before them):

$ cat in.txt #foo 3 bar 5 ;baz 7 $ datamash sum 2 < in.txt 15 $ datamash -C sum 2 < in.txt 5

## Multiple fields¶

Use comma or dash to specify multiple fields. The following are equivalent:$ seq 9 | paste - - - 1 2 3 4 5 6 7 8 9 $ seq 9 | paste - - - | datamash sum 1 sum 2 sum 3 12 15 18 $ seq 9 | paste - - - | datamash sum 1,2,3 12 15 18 $ seq 9 | paste - - - | datamash sum 1-3 12 15 18

## Rounding¶

The following demonstrate the different rounding operations:$ ( echo X ; seq -1.25 0.25 1.25 ) \ | datamash --full -H round 1 ceil 1 floor 1 trunc 1 frac 1 X round(X) ceil(X) floor(X) trunc(X) frac(X) -1.25 -1 -1 -2 -1 -0.25 -1.00 -1 -1 -1 -1 0 -0.75 -1 0 -1 0 -0.75 -0.50 -1 0 -1 0 -0.5 -0.25 0 0 -1 0 -0.25 0.00 0 0 0 0 0 0.25 0 1 0 0 0.25 0.50 1 1 0 0 0.5 0.75 1 1 0 0 0.75 1.00 1 1 1 1 0 1.25 1 2 1 1 0.25

## Reversing fields¶

$ seq 6 | paste - - |datamashreverse 2 1 4 3 6 5

## Transposing a file¶

$ seq 6 | paste - - |datamashtranspose 1 3 5 2 4 6

## Removing Duplicated lines¶

Remove lines with duplicate key value from field 1 (Unlike**first**,

**last**operations,

**rmdup**is much faster and does not require sorting the file with -s):

# Given a list of files and sample IDs: $ cat INPUT SampleID File 2 cc.txt 3 dd.txt 1 ab.txt 2 ee.txt 3 ff.txt # Remove lines with duplicated Sample-ID (field 1): $datamashrmdup 1 < INPUT # or use named field: $datamash-H rmdup SampleID < INPUT SampleID File 2 cc.txt 3 dd.txt 1 ab.txt

## Checksums¶

Calculate the sha1 hash value of each TXT file, after calculating the sha1 value of each file's content:$ sha1sum *.txt | datamash -Wf sha1 2

## Check file structure¶

Check the structure of the input file: ensure all lines have the same number of fields, or expected number of lines/fields:$ seq 10 | paste - - | datamash check && echo ok || echo fail 5 lines, 2 fields ok $ seq 13 | paste - - - | datamash check && echo ok || echo fail line 4 (3 fields): 10 11 12 line 5 (2 fields): 13 datamash: check failed: line 5 has 2 fields (previous line had 3) fail $ seq 10 | paste - - | datamash check 2 fields 5 lines 5 lines, 2 fields $ seq 10 | paste - - | datamash check 4 fields line 1 (2 fields): 1 2 datamash: check failed: line 1 has 2 fields (expecting 4) $ seq 10 | paste - - | datamash check 7 lines datamash: check failed: input had 5 lines (expecting 7)

## Cross-Tabulation¶

Cross-tabulation compares the relationship between two fields. Given the following input file:$ cat input.txt a x 3 a y 7 b x 21 a x 40

Show cross-tabulation between the first field (a/b) and the second field (x/y) - counting how many times each pair appears (note: sorting is required):

$datamash-s crosstab 1,2 < input.txt x y a 2 1 b 1 N/A

An optional grouping operation can be used instead of counting:

$datamash-s crosstab 1,2 sum 3 < input.txt x y a 43 7 b 21 N/A $datamash-s crosstab 1,2 unique 3 < input.txt x y a 3,40 7 b 21 N/A

## Binning numeric values¶

Bin input values into buckets of size 5:$ ( echo X ; seq -10 2.5 10 ) \ |datamash-H --full bin:5 1 X bin(X) -10.0 -15 -7.5 -10 -5.0 -10 -2.5 -5 0.0 0 2.5 0 5.0 5 7.5 5 10.0 10

## Binning string values¶

Hash any input value into a numeric integer. A typical usage would be to split an input file into N chunks, ensuring that all values of a certain key will be stored in the same chunk:$ cat input.txt PatientA 10 PatientB 11 PatientC 12 PatientA 14 PatientC 15

Each patient ID is hashed into a bin between 0 and 9 and printed in the last field:

$datamash--full strbin 1 < input.txt PatientA 10 5 PatientB 11 6 PatientC 12 7 PatientA 14 5 PatientC 15 7

Splitting the input into chunks can be done with awk:

$ cat input.txt \ |datamash--full strbin 1 \ | awk '{print > $NF ".txt"}'

# ADDITIONAL INFORMATION¶

See GNU Datamash Website (https://www.gnu.org/software/datamash)# AUTHOR¶

Written by Assaf Gordon.# COPYRIGHT¶

Copyright © 2018 Assaf Gordon License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

# SEE ALSO¶

The full documentation for**datamash**is maintained as a Texinfo manual. If the

**info**and

**datamash**programs are properly installed at your site, the command

**info datamash**

should give you access to the complete manual.

December 2018 | datamash 1.4 |