cuts
cuts: Unix/POSIX cut (and paste) on (s)teroids.
cut is a very useful Unix (and POSIX standard) utility designed to
extract columns from files. Unfortunately, despite its usefulness
and great popularity, it is pretty limited in power.
Many questions on stackoverflow
suggest that the same pain-points of the standard cut are felt by many users.
The following list demonstrates what is missing in cut and why
I felt the need to write cuts:
cuts automatically detects the file input column delimiter:
In ~90% of common cases there's no need to pass the delimiter. The other ~10% are covered via supported options.
#
# -- cut doesn't:
#
$ cut -f1 test.dat
0,1,2
0,1,2
0,1,2
#
# -- cuts does:
#
$ cuts 0 test.dat
0
0
0
As you can see, cuts uses zero-based indexing
(index 0 means 1st column) by default.
Accordingly, the examples below use 0-based indexing.
If you prefer 1-based indexing, like cut, you may easily
change the default, either via the command line (-0 option),
or more permanently, via a small config file ~/.cuts.pl,
which is read early during runtime (details below).
cuts supports mixed input delimiters (e.g. both CSV and TSV)
#
# -- a file with mixed delimiters
#
0,1,2
0 1 2
0 1 2
#
# -- cut doesn't "cut it":
#
cut -f2 t.mixed
0,1,2
0 1 2
1
#
# -- cuts does:
#
$ cuts 1 t.mixed
1
1
1
cuts does automatic side-by-side pasting
#
# -- cut doesn't output columns side-by-side when reading from
# multiple input files, even though this is the most useful
# and expected thing to do.
# (Requiring a separate utility like "paste")
#
#
# -- a simple example input
#
$ cat t.tsv
0 1 2
a b c
X Y Z
#
# -- cut does one file at a time:
#
$ cut -f2 t.tsv t.tsv
1
b
Y
1
b
Y
#
# -- cuts does automatic side-by-side printing, as expected:
#
$ cuts 1 t.tsv t.tsv
1 1
b b
Y Y
cuts supports multi-char column delimiters
In particular, standard cut can't deal with the common case
of any white-space sequence:
#
# -- a file with variable length space-delimiters
#
$ cat 012.txt
0 1 2
0 1 2
0 1 2
#
# -- standard cut doesn't "cut it":
#
$ cut -d' ' -f2 012.txt
#
# -- cuts does what makes sense
# while not requiring explict user action:
#
$ cuts 1 012.txt
1
1
1
cuts supports powerful, perl style, regexp delimiters
When your delimiter is a bit more complex (say, any sequence of non-digits)
and you have cut, you're out-of-luck. cuts fixes this by allowing you
to specify any perl regular-expression (regexp) as the delimiter:
#
# -- a file with numbers separated by mixed non-numeric chars
#
$ cat 012.regex
0-----1-------2
0 ## 1 #### 2
0 aa 1 bbbbbbb 2
#
# -- cuts accepts perl regexps for input delimiters
# in this case, we set the delimiter regexp to "any sequence of non-digits"
#
$ cuts -d '[^0-9]+' 1 012.regex
1
1
1
cuts supports negative (from-end) column numbers
This is useful when you have, say, 257 fields (but you haven't counted
them, so you don't really know), and you're interested in the last field,
or the one before the last, etc. cuts supports negative offsets
from the end:
#
# -- Ask cuts to print last field only, by using a negative offset
#
$ cuts -1 012.txt
2
2
2
cuts supports changing order of columns
Unlike cut which ignores the order requested by the user,
and always force-prints the fields in order from low to high:
#
# -- cut can't change the order of columns:
#
$ cut -f3,2,1 file.tsv
0 1 2
0 1 2
0 1 2
#
# -- cuts does exactly what you ask it to:
#
$ cuts 2 1 0 file.tsv
2 1 0
2 1 0
2 1 0
cuts is more powerful dealing with variable number of columns:
The ability to offset from the end of line, in combination with the
ability to specify perl regular expressions as delimiters makes some
jobs that would require writing specialized scripts,
straight-forward with cuts:
#
# -- Example file, Mary doesn't have a middle-initial
#
$ cat t.complex
firstname midinitial lastname phone-number Age
John T. Public 555-5555 35
Mary Joe 444-5555 27
#
# -- Want the phone-number? It's easy with cuts
#
$ cuts t.complex -2
phone-number
555-5555
444-5555
cuts forgives you if you accidentally use -t (like sort does)
It is unfortunate that the Unix toolset is so inconsistent in the
choice of option-letters. cuts solves this by allowing 'any of
the above' in these cases. So if you accidentally use -s instead of
-d because you think "separator" instead of "delimiter", or -t
instead of -d because you have the sort convention in your head,
cuts still works as you expect it to.
cuts requires minimal typing for simple column extraction tasks
cut is harder to use, and somewhat less friendly because it doesn't
support reasonable defaults. For example:
#
# -- `cut` errors when arguments are missing:
#
$ cut -d, example.csv
cut: you must specify a list of bytes, characters, or fields
#
# -- compare to cuts, where default is 1st field &
# field-delimiters are auto-detected for most common cases:
#
$ cuts example.csv
0
0
0
cuts supports multi-file & multi-column mixes
For example 2nd column from file1 and 3rd column from file2.
Obviously with the power of the bash shell you can do stuff like:
$ paste <(cut -d, -f1 file.csv) <(cut -d"<TAB>" -f2 file.tsv)
but that requires too much typing (3 commands, using SHIFTs on the keyboard, & shell-magic), while still not supporting regexp-style delimiters and offsets from end.
Compare the above to the simpler, and more intuitive, cuts version,
which works right out of the box, in any shell:
#
# -- example input:
#
$ cat file.tsv
0 1 2
a b c
#
# -- another example input, but with different delimiters
#
$ cat file.csv
0,1,2
a,b,c
# -- "cuts" does exactly what you ask it to,
# both slicing and joining as expected.
#
$ cuts file.csv 0 file.tsv 1
0 1
a b
cuts supports reverse-ranges and range wrap-arounds
#
# -- example input with variable number of columns
#
$ cat 1-20-wide.csv
0,1,2,3,4,5,6,7,8,9,10
0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15
0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20
#
# -- last 3 fields
#
$ cuts -3--1 1-20-wide.csv
8 9 10
13 14 15
18 19 20
#
# -- reverse order works too, as expected:
#
$ cuts -1--3 1-20-wide.csv
10 9 8
15 14 13
20 19 18
#
# -- and you can wrap-around the end (from negative to positive) too:
#
$ cuts -1-2 1-20-wide.csv
10 0 1 2
15 0 1 2
20 0 1 2
Other utilities, like awk or perl give you more power, at the expense
of having to learn a more complex language, to do what you want.
cuts is designed to give you the power you need in almost all cases,
while always being able to stay on the command line, and keeping
the human interface as simple and minimalist as possible
cuts arguments can be:
- file-names
- column-numbers (negative offsets from the end are supported too) or
- any combo of the two using: `file:colno`
Just like cut, cuts supports - as a handy alias for stdin.
cuts design principles
The following are the principles which guide the design decisions of cuts.
Reasonable defaults for everything
An unspecified file-name will default to /dev/stdin
so you can easily pipe any other command output into cuts.
An unspecified column-number will default to the 1st column (0)
A file-name without a column-number will cause the last specified column-number to be reused.
A column-number without a file-name will cause the last specified file-name to be reused.
By default, the input column delimiter is the most common case of
any-sequence of white-space or a comma, optionally surrounded by
white-space. As a result, in the vast majority of use cases, there's
no need to specify an input column delimiter at all. If you have
a more complex case you may override cuts default
input-field-delimiter:
$ cuts -d '<some-perl-regexp>' ...
# see `man perlre` for documentation on perl regular expressions
Similarly, the output column delimiter which is tab by default, can be
overridden using -T <sep> (or -S, or -D). This is chosen
as a mnemonic: lowercase options are for input delimiters, while
the respective upper-case options are for output delimiters.
Require minimal typing from the user
In addition to having reasonable defaults, cuts doesn't force you
to type more than needed, or enforce an order of arguments on you.
It tries to be as minimalist as possible in its requirements from the user.
Compare one of the simplest and most straightforward examples of
extracting 2 columns (first and third) from a single file:
# -- the traditional, cut way:
$ cut -d, -f 1,3 file.csv
# -- the cuts way: (over 25%) shorter & sweeter:
$ cuts file.csv 0 2
Minimal typing is also what guided the decision to include the
functionality of paste in cuts.
There's one exception to the cuts requires less typing: cut
allows half-ranges like -N to mean "up to Nth field", for
example -3 implies 1-3 (a small saving of a single character
when typing). Since cuts has to support negative offsets which
are much more important, IMHO, full ranges are required.
Input flexibility & tolerance to missing data
One thing that cuts does is try and be completely tolerant
and supportive to cases of missing data. If you try to paste two columns,
side-by-side, from two files but one of the files is shorter,
cuts will oblige and won't output a field where it is missing
from the shorter file, until it reaches EOF on the longer file.
Similarly, requesting column 2 (3rd column) when there are only 2 columns (0,1) in a line will result in an empty output for that field rather than resulting in a fatal error. This is done by design and it conforms to the perl philosophy of silently converting undefined values to empty ones.
Examples
cuts 0 file1 file2 Extract 1st (0) column from both files
cuts file1 file2 0 Same as above (flexible argument order)
cuts file1 file2 Same as above (0 is default colno)
cuts -1 f1 f2 f3 Last column from each of f1, f2, & f3
cuts file1:0 file2:-1 1st (0) column from file1 & last column from file2
cuts 0 2 3 Columns (0,2,3) from /dev/stdin
cuts f1 0 -1 f2 1st & last columns from f1
+ last column (last colno seen) from f2
cuts 3,5-8 f1 columns (3, 5, 6, 7, 8) (0-based) from f1
cuts 3,8-5 f1 Same as above, but 5-8 in reverse order
cuts -4--1 Last 4 columns as a range
cuts -2-3 Last 2 columns and 1st 4 columns (range wrap-around)
Usage
Simply call cuts without any argument to get a full usage message:
$ cuts
Usage: cuts [Options] [Column_Specs]...
Options:
-v verbose (mostly for debugging)
-0 Don't use the default 0-based indexing, use 1-based
-c Don't use personal config-file (even if exists)
Input column separator options (lowercase):
-d <sep> Use <sep> (perl regexp) as input column delimiter
-t/-s <sep> Handy aliases for -d
Output column separator options (mnemonic: uppercase of same):
-D <sep> Use <sep> (string) as output column delimiter
-T/-S <sep> Handy aliases for -D
Column_Specs:
filename:colno Extract colno from filename
filename Use filename to extract columns from
colno Use column colno to extract columns
If there's an excess of colno args, will duplicate the last
file arg. If there's an excess of file args, will duplicate
the last colno.
If omitted:
Default file is /dev/stdin
Default colno is 0 (or 1 if 1-based indexing is in effect)
Examples:
cuts 0 file1 file2 1st (0) column from both files
cuts file1 file2 0 Same as above (flexible argument order)
cuts file1 file2 Same as above (0 is default colno)
cuts -1 f1 f2 f3 Last column from each of f1, f2, & f3
cuts file1:0 file2:-1 1st column from file1 & last column from file2
cuts 0 2 3 Columns (0,2,3) from /dev/stdin
cuts f1 0 -1 f2 1st & last columns from f1
+ last column (last colno seen) from f2
cuts 3,5-8 f1 Columns (3, 5, 6, 7, 8) from f1
cuts 3,8-5 f1 Same as above, but 5-8 in reverse order
Further configuration & customization
If you don't like cuts defaults, you can override them in
an optional personal configuration file: ~/.cuts.pl
If this file exists, cuts will read it during startup allowing you
override cuts default parameters, in particular the value of
the $ICS input-column separator regexp. The syntax of this
file is perl:
# -- If you prefer 1-based indexing by default, set $opt_0 to 1.
# You may also set it from the command-line with the -0 option.
# This is a mnemonic: the -0 option means "disable 0-based".
our $opt_0 = 0;
# -- Default column to select, when unspecified
our $DefaultColno = 0;
# -- Alternative file:colno char separators
our $FCsep = ':%#';
# -- Default input column separator
# Smart matching of: CSV[+optional-spaces] / TSV / other-white-space
#
# For quoted CSV/TSV/SSV, you may try: -d '^"|"[, \t]"|"$'
# Also, see examples in the test-suite
our $ICS = '(?:\s*,\s*|\s+)';
# -- Default output column separator
our $OCS = "\t";
# -- if you use a config file, you must end it with 1;
# -- so executing it by cuts using perl 'do' succeeds.
1;
TODO items (contributions welcome)
I made no effort to make cuts fast. Although compared to the
I/O overhead, there may be not much need for it. If you have ideas
on how to make the column extractions and joining more efficient,
without compromising the simplicity, elegance and generality
of the code, that would be welcome.
Per file column input delimiters. I haven't had the need so far so
that took a back-seat in priority. The most common case of
intermixing TSV and CSV files as inputs is working thanks to
the current default multi-match pattern $ICS. $ICS simply
matches any of: multi-white-space, tabs, or (optionally space surrounded)
commas. This ensures that even an extreme case of a schizophrenic input like:
$ cat schizo.csv
0,1 , 2
0,1 ,2
0,1 ,2
a b c
Works correctly, and as designed/expected.
$ cuts -1 schizo.csv
2
2
2
c
Some may consider this non-purist. I consider it a blissful feature because it allows dealing with even poorly structured data-sets.
Implement cut rarely used options? I haven't had the need for
them, and if I ever do, I can simply use cut itself, so I haven't
tried to implement fixed-width field support, byte-offsets,
--complement, --characters. The basic features that cut
is missing were much more critical for me when writing cuts.
Bugs & Limitations
The most notable remaining issues with cuts are (IMHO):
- Ranges going from positive to negative offsets, e.g.
2--3are interpreted as in reverse order (because 2 > -3). The result is a wrapped-around the beginning index-set. This is good because is consistent with the symmetric wrap-around-the-end case of say, -3-2. OTOH: it is bad because it is not the natural human-way of interpreting negative indexes as being higher (near the end of the line). - Speed (vs compiled C)
- Unexpected results if your data has tabs, spaces, and/or commas within fields. This is a deliberate design decision (optimize for the most common case.) that can be easily worked-around. If you don't like the default, you can either:
- Pass a different delimiter using:
-d 'regexp' - Make your choice permanent via the personal config file
~/.cuts.pland the$ICS(Input Column Separator) variable.
- Pass a different delimiter using:
Other thoughts & notes
Should the default $ICS be extended?
To also cover :, ;?
Other punctuation chars?
I am not sure. For some people who regularly use data-sets with these chars as delimiters, it makes sense, but for the vast majority of users, the current simple (and minimalistic) default should work well.
Why do I support the filename:colno syntax?
It seems redundant (since filename colno works just as well.)
The reason is that sometimes you may have files named 1, 2 etc.
This introduces an ambiguity: are these arguments files or column numbers?
cuts solves this ambiguity by:
- Giving priority to files (it first checks arguments for file existence)
- In case you want to force
1to a column number, even in the presence of a file by the same name, you can use thefile:colnosyntax. - You may even use
#, or%, as thefile:colnoseparator instead of:for somewhat greater control.
Resolving option ambiguity
Negative column offsets and - for stdin don't play well
with getopts() because the code can no longer assume that what
starts with - is an option and not an argument.
cuts solves this by auto injecting -- (end of options marker)
into @ARGV before calling getopts (if needed). This is so the
user never has to worry about the ambiguity. For example, (-v is
cuts own debugging/verbose option, while -3 is a column index
specifier), still this works as expected because cuts
disambiguates them correctly:
$ cuts -v -3 file.txt
Test suite
cuts comes with an extensive test suite to ensure
that it behaves as designed, and that changes don't cause regressions.
Running make in the top source directory or in the tests
sub-directory will run the test suite.
Historical perspective
cut is one of the earliest Unix utilities
with over 40 years of history. It's top weaknesses of single char
delimiters and no support for regexps are a likely a direct result
of being written so early. What is surprising is that in 40 years
no significant improvement to it has been introduced, in particular,
when POSIX, and the free GNU implementation came about.
Other implementations of improved cut
Before diving into coding I searched the web for alternatives. I found a few, unsurprisingly, most written in perl, but none of them were what I was looking for.
I basically wanted an enhanced cut, i.e. a tool that fixes
the top pain-points in cut rather than a new beast altogether.
I was looking for a strong combination of power and simplicity. Even more so: I wanted more power, but a simpler interface which at first looked contradictory, but turned out to be possible.
Replacements that were too weak: e.g. missing ranges, or missing negative offsets, or too complex: requiring a big manual nearby, or having a long list of options that were cobbled together ad-hoc, were out. So I just had to write my own.
Feedback
If you like cuts, please send me an email via github.2009
.at. yendor.com
If you don't, cuts is free software and it is hosted on github,
so consider forking, and fixing it. If you don't know how to code,
and feel that I should fix it, please email anyway, or open an
"issue" on github. Any comment, good a bad, is highly appreciated.
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