<commit_before>MartScript
==========

MartScript is a simple non-branching imperative scripting language
for creating BioMarts automatically (i.e. non-interactively). The
language supports

 * extending Ensembl databases with custom data
 * automatisation of MartBuilder/MartEditor functionality
 * the creation and execution of a mart's SQL-commands

This is a fully functional release of MartScript as a beta version,
mainly due to the lack of documentation (will follow 'shortly') and
some minor cosmetic issues. However, we used MartScript in production
to create: [www.pubmed2ensembl.org](http://www.pubmed2ensembl.org)

---

License
=======

MartScript itself is released under the 2-clause BSD License (see below),
but I am also redistributing the partially modified code of MartBuilder
and MartScript here, as well as JAR files of several libraries that are
necessary to run MartScript. MartBuilder, MartEditor and the JAR-packaged
files come with their own licenses that should be looked up on their
originating web-sites.

MartScript License
------------------

Redistribution and use in source and binary forms, with
or without modification, are permitted provided that the
following conditions are met:

1. Redistributions of source code must retain the above
   copyright notice, this list of conditions and the
   following disclaimer.
2. Redistributions in binary form must reproduce the above
   copyright notice, this list of conditions and the
   following disclaimer in the documentation and/or other
   materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.<commit_msg>Edited README.markdown<commit_after>MartScript
==========

MartScript is a simple non-branching imperative scripting language
for creating BioMarts automatically (i.e. non-interactively). The
language supports

 * extending Ensembl databases with custom data
 * automatisation of MartBuilder/MartEditor functionality
 * the creation and execution of a mart's SQL-commands

This is a fully functional release of MartScript as a beta version,
mainly due to the lack of documentation (will follow 'shortly') and
some minor cosmetic issues. However, we used MartScript in production
to create: [www.pubmed2ensembl.org](http://www.pubmed2ensembl.org)

Supporting Software
-------------------

MartScript depends on partially modified code of MartBuilder as well as as 
JAR files of several libraries that from the BioMart project, which are 
redistributed here. MartBuilder, MartEditor and the JAR-packaged files 
are released under LGPL.

License
-------

MartScript itself is released under the 2-clause BSD License.

Copyright  2010, The University of Manchester. 
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are
permitted provided that the following conditions are met:

   1. Redistributions of source code must retain the above copyright notice, this list of
      conditions and the following disclaimer.

   2. Redistributions in binary form must reproduce the above copyright notice, this list
      of conditions and the following disclaimer in the documentation and/or other materials
      provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

The views and conclusions contained in the software and documentation are those of the
authors and should not be interpreted as representing official policies, either expressed
or implied, of the University of Manchester.

{'fraction_non_alphanumeric': 0.049959049959049956, 'fraction_numerical': 0.0028665028665028664, 'mean_word_length': 4.726846424384525, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2432551', 'n_tokens_mistral': 1234, 'n_tokens_neox': 1123, 'n_words': 663}