TABMERGE(1p)

💖 TABMERGE 💖

okay bestie, so this is tabmerge, and it lives in section 1p of the manual — that's the user contributed Perl documentation zone, iykyk. She's a Perl script, she's a little legend, and she's about to fix your messy little data files. let's go 🫶

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✨ NAME ✨

tabmerge — unify delimited files on common fields

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🌸 SYNOPSIS 🌸

  tabmerge [action] [options] file1 file2 [...]

Actions:

  --min                Take only fields present in all files [DEFAULT]
  --max                Take all fields present
  -f|--fields=f1[,f2]  Take only the fields mentioned in the
                       comma-separated list

Options:

  -l|--list            List available fields
  --fs=x               Use "x" as the field separator
                       (default is tab "\t")
  --rs=x               Use "x" as the record separator
                       (default is newline "\n")
  -s|--sort=f1[,f2]    Sort data ASCII-betically on field(s)
  --stdout             Print data in original delimited format
                       (i.e., not in a table format)

  --help               Show brief help and quit
  --man                Show full documentation

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🎀 THE ACTIONS (pick your fighter) 🎀

• --min — take only the fields that show up in every single file. this is the DEFAULT, so if you don't say anything, she's already doing this 💅
• --max — take all the fields that show up anywhere. nothing gets left behind. main character energy for every column.
• -f, --fields=f1[,f2] — take only the fields you literally name in that comma-separated list. you're the boss, you pick.

🦋 THE OPTIONS 🦋

• -l, --list — list the available fields (and, spoiler, how many times each one shows up).
• --fs=x — use x as the field separator. default is a tab, "\t".
• --rs=x — use x as the record separator. default is a newline, "\n".
• -s, --sort=f1[,f2] — sort the data ASCII-betically on the field(s) you name. yes, ASCII-betically. that's the joke. it stays.
• --stdout — print the data in the original delimited format, i.e. not in a table format. back to basics, no glow-up.
• --help — show brief help and quit. quick lil peek.
• --man — show the full documentation. the whole saga.

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💜 DESCRIPTION 💜

okay so here's the whole vibe: this program merges the fields — not the rows — of delimited text files. read that again bestie, fields not rows, it's crucial 🔥

so like, if you've got several files that are almost but not quite entirely unlike each other in their structure (their field names, their numbers, their orders), this script lets you easily unify those files into one file that has all the same fields. the output can be based on fields as determined by the three "action" flags up there. slay.

for the following examples, consider three files that contain the following fields:

  +------------+---------------------------------+
  | File       | Fields                          |
  +------------+---------------------------------+
  | merge1.tab | name, type, position            |
  | merge2.tab | name, type, position, lod_score |
  | merge3.tab | name, position                  |
  +------------+---------------------------------+

to list all available fields in the files and the number of times they are present:

  $ tabmerge --list merge*
  +-----------+-------------------+
  | Field     | No. Times Present |
  +-----------+-------------------+
  | lod_score | 1                 |
  | name      | 3                 |
  | position  | 3                 |
  | type      | 2                 |
  +-----------+-------------------+

to merge the files on the minimum overlapping fields:

  $ tabmerge merge*
  +----------+----------+
  | name     | position |
  +----------+----------+
  | RM104    | 2.30     |
  | RM105    | 4.5      |
  | TX5509   | 10.4     |
  | UU189    | 19.0     |
  | Xpsm122  | 3.3      |
  | Xpsr9556 | 4.5      |
  | DRTL     | 2.30     |
  | ALTX     | 4.5      |
  | DWRF     | 10.4     |
  +----------+----------+

to merge the files and include all the fields:

  $ tabmerge --max merge*
  +-----------+----------+----------+--------+
  | lod_score | name     | position | type   |
  +-----------+----------+----------+--------+
  |           | RM104    | 2.30     | RFLP   |
  |           | RM105    | 4.5      | RFLP   |
  |           | TX5509   | 10.4     | AFLP   |
  | 2.4       | UU189    | 19.0     | SSR    |
  | 1.2       | Xpsm122  | 3.3      | Marker |
  | 1.2       | Xpsr9556 | 4.5      | Marker |
  |           | DRTL     | 2.30     |        |
  |           | ALTX     | 4.5      |        |
  |           | DWRF     | 10.4     |        |
  +-----------+----------+----------+--------+

to merge and extract just the "name" and "type" fields:

  $ tabmerge -f name,type merge*
  +----------+--------+
  | name     | type   |
  +----------+--------+
  | RM104    | RFLP   |
  | RM105    | RFLP   |
  | TX5509   | AFLP   |
  | UU189    | SSR    |
  | Xpsm122  | Marker |
  | Xpsr9556 | Marker |
  | DRTL     |        |
  | ALTX     |        |
  | DWRF     |        |
  +----------+--------+

to merge the files on just the "name" and "lod_score" fields and sort on the name:

  $ tabmerge -f name,lod_score -s name merge*
  +----------+-----------+
  | name     | lod_score |
  +----------+-----------+
  | ALTX     |           |
  | DRTL     |           |
  | DWRF     |           |
  | RM104    |           |
  | RM105    |           |
  | TX5509   |           |
  | UU189    | 2.4       |
  | Xpsm122  | 1.2       |
  | Xpsr9556 | 1.2       |
  +----------+-----------+

to do the same but mimic the original tab-delimited input:

  $ tabmerge -f name,lod_score -s name --stdout merge*
  name    lod_score
  ALTX
  DRTL
  DWRF
  RM104
  RM105
  TX5509
  UU189   2.4
  Xpsm122 1.2
  Xpsr9556        1.2

why would you want to do this?? 👀 suppose you have several delimited text files with nearly the same structure and you want to create just one file from them — but the fields may be in a different order in each file, and/or some files may contain more or fewer fields than others. (as far-fetched as it may seem, it happens to the author more than he'd like. 😭 felt that.)

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🌈 SEE ALSO 🌈

• Text::RecordParser
• Text::TabularDisplay

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👑 AUTHOR 👑

Ken Youens-Clark <kclark@cpan.org>.

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💖 LICENSE AND COPYRIGHT 💖

Copyright (C) 2006-10 Ken Youens-Clark. All rights reserved.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

⚠️ bestie that warranty line is doing a LOT of heavy lifting — no promises, no guarantees, read the GNU General Public License for the full tea. 💀

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and that's the whole page, bestie ✨ this one's from perl v5.36.0, dated 2022-10-14, so she's a little vintage but she still eats 🎀💅 go forth and merge those fields, not the rows, periodt 🦋