HPR4687: UNIX Curio #11 - Merging Files

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ether

This series is dedicated to exploring little-known—and occasionally useful—trinkets lurking in the dusty corners of UNIX-like operating systems.

I frequently find myself reaching for the
cut
utility when writing scripts to extract one piece of data from a line, or to select specific fields from a log file. While I am familiar with its counterpart,
paste
, I don't employ it very often because I don't typically need its functionality.

This perhaps has to do with the fact that I rarely work with text files containing lists. For shorter lists, I usually end up using a spreadsheet and for larger ones, a relational database. Both are valuable tools with their own strengths and weaknesses, but it is good to also know about standard utilities for working with lists. After uploading UNIX Curio #8 (




¹
, but can explain how it works. Briefly, it is a rough opposite of
cut
—when given multiple files as arguments, it assembles the first line from each one separated by tabs, then the second line, and so on. Instead of tabs, a different delimiter can be chosen with the
-d
option. Another option is
-s
, which swaps rows and columns so that the contents of each named file would appear on one line. While
paste
itself doesn't qualify as a UNIX Curio in my opinion, there is one feature that does: a hyphen can be given as an argument multiple times. In this special case, the output is taken line by line from standard input, but is spread across as many columns as there are hyphens.

Example of using




paste




to turn the output of




ls




into columns. Because these columns are separated by tabs, they don't necessarily line up when a filename is eight or more characters long. The




-1




is not required for the second




ls




command since that behavior is implied when output isn't going to a terminal. The




-C




option to




ls




usually gives nicer-looking output on a terminal—also, it lists in ascending order down by column. (Most implementations default to




-C




when output goes to a terminal.) If you want items ascending along rows like the




paste




example does, try




ls -x




instead.

$ ls -1 /proc/net

anycast6

arp

bnep

connector

dev

dev_mcast

dev_snmp6

fib_trie

fib_triestat

hci

icmp

icmp6

if_inet6

igmp

igmp6

ip6_flowlabel

ip6_mr_cache

ip6_mr_vif

ip_mr_cache

ip_mr_vif

ip_tables_matches

ip_tables_names

[...35 more entries not shown...]

$ ls /proc/net | paste - - - -

anycast6        arp     bnep    connector

dev     dev_mcast       dev_snmp6       fib_trie

fib_triestat    hci     icmp    icmp6

if_inet6        igmp    igmp6   ip6_flowlabel

ip6_mr_cache    ip6_mr_vif      ip_mr_cache     ip_mr_vif

ip_tables_matches       ip_tables_names ip_tables_targets       ipv6_route

l2cap   mcfilter        mcfilter6       netfilter

netlink netstat packet  protocols

psched  ptype   raw     raw6

rfcomm  route   rt6_stats       rt_acct

rt_cache        sco     snmp    snmp6

sockstat        sockstat6       softnet_stat    stat

tcp     tcp6    udp     udp6

udplite udplite6        unix    wireless

xfrm_stat

$ ls -C /proc/net

anycast6      if_inet6           l2cap      rfcomm        tcp

arp           igmp               mcfilter   route         tcp6

bnep          igmp6              mcfilter6  rt6_stats     udp

connector     ip6_flowlabel      netfilter  rt_acct       udp6

dev           ip6_mr_cache       netlink    rt_cache      udplite

dev_mcast     ip6_mr_vif         netstat    sco           udplite6

dev_snmp6     ip_mr_cache        packet     snmp          unix

fib_trie      ip_mr_vif          protocols  snmp6         wireless

fib_triestat  ip_tables_matches  psched     sockstat      xfrm_stat

hci           ip_tables_names    ptype      sockstat6

icmp          ip_tables_targets  raw        softnet_stat

icmp6         ipv6_route         raw6       stat

$ ls -x /proc/net

anycast6           arp              bnep               connector     dev

dev_mcast          dev_snmp6        fib_trie           fib_triestat  hci

icmp               icmp6            if_inet6           igmp          igmp6

ip6_flowlabel      ip6_mr_cache     ip6_mr_vif         ip_mr_cache   ip_mr_vif

ip_tables_matches  ip_tables_names  ip_tables_targets  ipv6_route    l2cap

mcfilter           mcfilter6        netfilter          netlink       netstat

packet             protocols        psched             ptype         raw

raw6               rfcomm           route              rt6_stats     rt_acct

rt_cache           sco              snmp               snmp6         sockstat

sockstat6          softnet_stat     stat               tcp           tcp6

udp                udp6             udplite            udplite6      unix

wireless           xfrm_stat

The
paste
command has limitations—the files you give it must all be already arranged in the same order, and if any file is missing a value, it must have a blank line so that subsequent lines will match up correctly. The files do
not
necessarily have to be sorted alphabetically, but whatever order they are in has to be the same. Check out HPR episodes
for some more background on the
paste
utility.

Example of using




paste




with files where some values are empty. Bob works from home so doesn't have an office assigned, and the laboratory Carol works in doesn't have a phone. This relies on the fact that the same line number in every file relates to the same person/entry.

$ cat names

Alice

Bob

Carol

Dave

$ cat offices

203



Lab6A

117

$ cat phones

+1 212-555-1234

+1 919-555-2345



+1 212-555-1278

$ paste names offices phones

Alice   203     +1 212-555-1234

Bob             +1 919-555-2345

Carol   Lab6A

Dave    117     +1 212-555-1278

Our second UNIX Curio for today is




²
, which has a bit more sophistication. It operates on two files, which can have multiple columns, and combines them using the join field. By default, the first column/field in each file is the join field, and only entries that exist in both files are printed. The
-1
and
-2
options can be used to join on a different field, and
-o
selects specific fields to be output. To make it so lines with missing entries also appear, you need to use the
-a
option, but an actual empty string with separator won't be printed unless
-o
is also present and includes the field.

The default field separator character is one or more "blanks" in the current locale—for the POSIX locale, this means a space or a horizontal tab. The
-t
option selects a different character and also removes the treatment of multiple occurrences as a single separator, making it possible to have an empty field in one or both of the files. By default, a single space is used to separate fields in the output. If
-t
is given, the same character is used for separating fields in both input and output. You would need to pipe output through another tool like
tr
if you wanted to have a different separator in the output.

The
join
utility might be an improvement over
paste
in some cases, since the join field makes it a little easier to identify which entries match up across files. It is limited to operating only on two files (one of which can be standard input), so combining more than that requires either creating temporary intermediate files or chaining together
join
commands in a pipeline. Another requirement is that all files must already be sorted in the current locale.

Example showing how




join




can be used with two tab-separated lists. The LC_ALL assignment forces




join




to sort using the C (POSIX) locale instead of whatever might be set in your environment. The "@" on the header line has no special meaning; it is just there to make sure it sorts before any letters or numbers (in the C locale; it might not in other locales). Note that if




-t




were not specified,
plist
would be treated as having three fields because of the space separating the country code from the rest of the phone number.

$ export tab="$(printf '\t')" #To more easily use tab characters below

$ cat olist

@Name   Office

Alice   203

Carol   Lab6A

Dave    117

$ cat plist

@Name   Phone

Alice   +1 212-555-1234

Bob     +1 919-555-2345

Dave    +1 212-555-1278

$ LC_ALL=C join -t "$tab" olist plist

@Name   Office  Phone

Alice   203     +1 212-555-1234

Dave    117     +1 212-555-1278

$ LC_ALL=C join -t "$tab" -a 1 -a 2 olist plist

@Name   Office  Phone

Alice   203     +1 212-555-1234

Bob     +1 919-555-2345

Carol   Lab6A

Dave    117     +1 212-555-1278

$ #By default, join acts as if empty fields don't exist; use -o to include

$ LC_ALL=C join -t "$tab" -a 1 -a 2 -o 0,1.2,2.2 olist plist

@Name   Office  Phone

Alice   203     +1 212-555-1234

Bob             +1 919-555-2345

Carol   Lab6A

Dave    117     +1 212-555-1278

$ #The -e option sets a placeholder to use for empty fields

$ LC_ALL=C join -t "$tab" -e "(none)" -a 1 -a 2 -o 0,1.2,2.2 olist plist

@Name   Office  Phone

Alice   203     +1 212-555-1234

Bob     (none)  +1 919-555-2345

Carol   Lab6A   (none)

Dave    117     +1 212-555-1278

The brief description for
join
is "relational database operator"—I won't dispute that, but in my view it offers far fewer capabilities than people would expect from today's relational databases. I would imagine that when most people think of those they have Structured Query Language (SQL) in mind, which offers a lot more flexibility and functions to operate on data. However, I can see how
join
could be suitable for simple operations.

Our last UNIX Curio for today relates to






⁴
in 1973. What
did
come as a shock to me is that both
cut
and




5
, and were actually preceded by




6
from 1979. I assumed that at least
cut
would have been around far earlier, given its usefulness and how firmly established it is, but I suppose it just
seems
to have been with us forever.