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README.md

Test Data Suite

This little suite helps you to manage test data.

Requirements

Before you start

Genome data must be converted into special formats, which is handled by the utility program 'twoBitsToFa'. Before you can download any data, be sure to set the executable bit of this program, i.e. call chmod a+x twoBitsToFa.

The software uses the Succinct Data Structure Library sdsl-lite by Simon Gog.

After installing sdsl lite, you can either

  • set up an environment variable called SDSLLITE that specifies the path to the library using the command export SDSLLITE="path/to/sdsllite/".
  • modify the file Make.helper in the root directory such that the uppermost path points to the Make.helper file of your sdsl-lite installation.

Test Data

Test data sorted by text corpora can be found in the file data.config. You may include this file to your own makefile to have references to all files of a certain text corpus. This suite includes the following text corpora:

A file with statistics about the test data can be found at here.

Usage

  • To load all included test files, call make.
  • To fully load a corpus cpname, use make cpname.
  • To download only a specific file named fname of corpus cpname, use make cpname/fname.
  • To clean data of a text corpus cpname, use make clean-cpname.
  • To clean all data, use make cleanall

Additional Notes

You may wish to include the file data.config to your own Makefile, so the data paths immediately are present. However, when loading data, always use the makefile in this directory and DO NOT include it, because it uses relative paths (possibly use cd data;make cpname/fname1 cpname/fname2 ... to load your data before using it).

Utility

A little utility program named filestat.cpp is included: it computes alphabet and file size for a given file. To get detailed file statistics in form of a PDF file, call make statistics.