GBGET(1)

💖 GBGET(1) — the basic data extraction & manipulation tool 💖

okay bestie, listen UP, because this one is genuinely iconic. This is the manual page for gbget, a User Command (section 1 of the manual, iykyk), and it's about to become your new main character. 🎀

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✨ NAME ✨

gbget — Basic data extraction and manipulation tool 🦋

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🌸 SYNOPSIS 🌸

gbget [options] 'filename[index](C,R)trans'

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💅 DESCRIPTION 💅

So basically? gbget prints slices of tabular data from files, and then it applies transformations to them. That's the whole vibe. ✨

Data get read from text files where the fields are separated by a space — and if you want a different separator, bestie, just use option -F. 🌈

Inside a data file, data-blocks are separated by two empty lines. Also, the file can be compressed with zlib (.gz), because we support that. 💖

Now let's break down every single piece of that synopsis, because you will need all of it:

• filename — this is the input file. If you don't specify it, it defaults to stdin, or to the last specified filename if there was one. 🫶
• index — stands for a data-block index.
• index — stands for a data-block index. (yes girl, it says it twice. I don't make the rules. 💀)
• C,R — stands for columns and rows spec, given as "min:max:skip", which selects from min to max every skip steps. If min and max are negative, they get counted from the end. By default all data are printed ("1:-1:1"). And here's the twist: if min>max, then the count is reversed and skip must be negative (-1 by default). Different specs are separated by semicolon ; and are considered sequentially. 🔥
• trans — is a list of transformations applied to the selected data. The roster is:
  • d — take the diff of subsequent columns
  • D — remove all rows with at least one Not-A-Number (NAN) entry
  • f — flatten the output, piling all columns
  • l — take log of all entries
  • P — print all entries collected as a data-block
  • t — transpose the matrix of data
  • z — subtract from the entries in each column their mean
  • Z — replace the entry in each column with their zscore
  • w — divide the entry in each column by their mean
  • '<..;..>' — functions separated by semicolons in angle brackets can be used for generic data transformation; the function is computed for each row of data. Variable names are x followed by the number of the column, and optionally by l and the number of lags. For instance x2+x3l1 means the sum of the entries in the 2nd column plus the entries in the 3rd column in the previous row. And x0 stands for the row number, while x is equal to x1. 🧚
  • '<@..;..>' — if the functions specification starts with a @, the functions are computed recursively along the columns. In this case the number after the x is the relative column, counted starting from the one considered at each step. ⭐
  • '{...}' — a function in curly brackets can be used to select data: only rows that return a non-negative value are retained. 👑

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✨ OPTIONS ✨

• -F — set the input fields separators (default ' \t') 🌸
• -o — set the output format (default '%12.6e') 💜
• -e — set the output format for empty fields (default '%13s') 🎀
• -s — set the output separation string (default ' ') 🌈
• -t — define global transformations applied before each output (default '') 💖
• -v — verbose mode 🦋

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🔥 EXAMPLES 🔥

Okay this is the part where it all clicks, watch:

gbget 'file(1:3)ld'

select the first three columns in file, take the log and the difference of successive columns; ✨

gbget 'file(2,-10:-1)
       <x^2> select the last ten elements of the second' of 'file' and
       print their squares

select the last ten elements of the second' of file and print their squares 💅

gbget '[2]()' '[1]()' < ...

select the second and first data block from the standard input. 🫶

gbget 'file(1:3)<x1*x2-x3>'

select the first three columns in file and in each row multiply the first two entries and. subtract the third. 😭

gbget 'file()<@x1+x2>'

print the sum of two subsequent columns 🔥

gbget 'file(1:3){x2-2}'

select the first three columns in file for the rows whose second field is not lower then 2 👑

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🌸 AUTHOR 🌸

Written by Giulio Bottazzi 💖

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🎀 REPORTING BUGS 🎀

Report bugs to <gbutils@googlegroups.com> — yes, fr fr, tell them everything. 🙈

Package home page: <http://cafim.sssup.it/~giulio/software/gbutils/index.html> 🌐

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💜 COPYRIGHT 💜

Copyright © 2001-2018 Giulio Bottazzi. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License (version 2) as published by the Free Software Foundation; ⭐

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. ⚠️ (no cap, read the license, bestie)

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and that's the whole page, you ate it, periodt 💅✨

This is gbget version 6.2, dated June 2021 — that's the source and the date for ya, and yes, this manual page is filed under GBGET(1) in the User Commands section. Go forth and slice that data, queen. 👑🦋🎀