<commit_before>=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=head1 CONTACT

 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
    
=cut

=head1 NAME

 FATHMM

=head1 SYNOPSIS

 mv FATHMM.pm ~/.vep/Plugins
 ./vep -i variations.vcf --plugin FATHMM,"python /path/to/fathmm/fathmm.py"

=head1 DESCRIPTION

 A VEP plugin that gets FATHMM scores and predictions for missense variants.
 
 You will need the fathmm.py script and its dependencies (Python, Python
 MySQLdb). You should create a "config.ini" file in the same directory as the
 fathmm.py script with the database connection options. More information about
 how to set up FATHMM can be found on the FATHMM website at
 https://github.com/HAShihab/fathmm.
 
 A typical installation could consist of:
 
 > wget https://raw.github.com/HAShihab/fathmm/master/cgi-bin/fathmm.py
 > wget ftp://supfam2.cs.bris.ac.uk/FATHMM/database/fathmm.v2.1.SQL
 > mysql -h[host] -P[port] -u[user] -p[pass] -e"CREATE DATABASE fathmm"
 > mysql -h[host] -P[port] -u[user] -p[pass] -Dfathmm < fathmm.v2.1.SQL
 > echo "[DATABASE]\nHOST = [host]\nPORT = [port]\nUSER = [user]\nPASSWD = [pass]\nDB = fathmm\n" > config.ini

=cut
<commit_msg>update version<commit_after>=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=head1 CONTACT

 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
    
=cut

=head1 NAME

 FATHMM

=head1 SYNOPSIS

 mv FATHMM.pm ~/.vep/Plugins
 ./vep -i variations.vcf --plugin FATHMM,"python /path/to/fathmm/fathmm.py"

=head1 DESCRIPTION

 A VEP plugin that gets FATHMM scores and predictions for missense variants.
 
 You will need the fathmm.py script and its dependencies (Python, Python
 MySQLdb). You should create a "config.ini" file in the same directory as the
 fathmm.py script with the database connection options. More information about
 how to set up FATHMM can be found on the FATHMM website at
 https://github.com/HAShihab/fathmm.
 
 A typical installation could consist of:
 
 > wget https://raw.github.com/HAShihab/fathmm/master/cgi-bin/fathmm.py
 > wget http://fathmm.biocompute.org.uk/database/fathmm.v2.3.SQL.gz
 > mysql -h[host] -P[port] -u[user] -p[pass] -e"CREATE DATABASE fathmm"
 > mysql -h[host] -P[port] -u[user] -p[pass] -Dfathmm < fathmm.v2.3.SQL
 > echo -e "[DATABASE]\nHOST = [host]\nPORT = [port]\nUSER = [user]\nPASSWD = [pass]\nDB = fathmm\n" > config.ini

=cut

{'fraction_non_alphanumeric': 0.09712425393380358, 'fraction_numerical': 0.016006511123168747, 'mean_word_length': 4.05761316872428, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 17, 'https://': 4, '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': '3412577', 'n_tokens_mistral': 1258, 'n_tokens_neox': 1165, 'n_words': 424}