Contents
tblutils contains several utilities to work with tabular text files: files containing tabular data written in plain text, with one row per line and columns separated by a common character (usually TAB or semicolon).
tblutils complements the usual unix tools like cut and paste by providing enhanced versions that support column labels through-out, so that you can extract columns by name (tblcut), filter data using a mathematical expression (tblfilter), re-order columns without caring about the column index (tblcsort), join multiple files on a common index without having to pre-sort them (tblmerge), and much more.
This project doesn’t have a fixed release schedule yet. All the relevant source/developer information can be found on Github.
You can download the latest sources directly with:
https://github.com/EuracBiomedicalResearch/tblutils/archive/master.zip
| tbl2excel: | Generate Excel files directly from tabular text files, without causing the typical conversion errors that happen when opening a text file directly from Excel. |
|---|---|
| tblabelize: | Assign automatic labels (header) to an unlabeled tabular text file. |
| tblunlabelize: | Remove labels from a tabular text file file. |
| tblcsort: | Sort/reorder the columns of a tabular text file by name. |
| tblcut: | Extract columns from tabular text files by name. |
| tblfilter: | Filters rows of a tabular text file using column names and regular/mathematical expressions. |
| tblmerge: | Merge/compare two tabular text files together using a common index/column name. |
| tblmerge2: | Merge two or more tabular text files together using a common index/column name (faster C implementation). |
| tblnorm: | Normalize a tabular text file (reorders both columns and rows). Generally used to make two files easier to compare. |
| tblsize: | Get a tabular text file width (column) and height (row count). |
| tbltransp: | Transpose a tabular text file (flip columns/rows). |
| tbltransp2: | Transpose a tabular text file (faster C implementation). |
| tbltomatrix: | Write a matrix using a three-column associative table. |
| tbl2tbl: | Convert CSV files to simple tabular, tab-separated text files (TSV) and back, fixing quoting/escaping along the way. |
| tblsubsplit: | Expand the contents of a column which contains multiple values into multiple rows, making it uniform and easier to process. |
| tblsubmerge: | Reverses the effect of tblsubsplit, merging values spanning across multiple rows into a single line/cell containing all the values. |
Full documentation is available for each tool inside the doc/ directory.
On Debian/Ubuntu, after unpacking the sources, type:
sudo apt-get install libtext-csv-xs-perl libexcel-writer-xlsx-perl libspreadsheet-writeexcel-perl sudo make install
to install all the required Perl modules and utilities to /usr/local/bin.
On other systems (Mac, other linux listributions), you can use cpan to install the required Perl modules instead:
sudo cpan -i Text::CSV_XS Spreadsheet::WriteExcel Excel::Writer::XLSX sudo make install
You can install all the utilities as a normal user by executing:
cpan -i Text::CSV_XS Spreadsheet::WriteExcel Excel::Writer::XLSX make PREFIX=$HOME/.local install
This will install all the utilities and Perl modules into your home directory (inside ~/.local/bin). Be sure to add this directory to your PATH (if not already present as a default) by running:
PATH="$PATH:$HOME/.local/bin"
You can make this change permanent by adding the above line to your ~/.profile script.
You can change the column separator by setting the TBLSEP environment variable as follows:
export TBLSEP=';'
The default separator, if not specified, is TAB. If you use Excel to export your data, you should use the save as type “Text (Tab delimited) (*.txt)” when doing “Save as …” to create a file compatible with the table utilities.
The command line flag -d (when supported) takes precedence over the environment variable.
Files are read and written with the same separator. If you need to change the separator, use tbl2tbl.
All the tools assume that the first line of any file contains column labels. You always refer to columns by labels, not numbers. Some tools support the -H flag to work with column numbers instead, in which case the first column is always 1. You can (should) use tblabelize to assign labels to an existing file.
You can open the standard input by using ‘-‘ instead of a named file. This is not universally supported by all tools.
tblutils was developed out of necessity during my work in bioinformatics. Perhaps surprisingly, the foundation of science is not some fancy HDF file or a complex database; but just a lousy, flat, loosely defined text file. In genetics these files are of gigabytes in size, and usually come by the thousands. A lot of time is dedicated to convert one text format to a slightly different one, munge IDs to make them acceptable by some analysis software, slice, dice, read and aggregate the results.
tblutils is a collection of tools that aim to complement the conventional unix text-processing tools, allowing the user to focus on the data while still allowing powerful scripting capabilities directly from the command line. We refer to columns by label, not by number. We want to compare numbers with mathematical operators, not regular expressions. By processing the files line-by-line as opposed to loading them in full, these tools work with unbounded file sizes, with pipes, with any compressed file format and can be run in parallel with zero effort.
We tried to set some conventions, such as mimicking the traditional unix tools when possible and re-use the same flags for equivalent meaning, but it’s not always the case. We will fix/improve the tools and documentation with time. Sometimes multiple implementations are provided, making different memory/disk/complexity trade-offs.
tblutils can be found at https://www.thregr.org/wavexx/software/tblutils/
tblutils‘s GIT repository is publicly accessible at: