<commit_before>#!/usr/bin/env perl

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

# modified by <NAME> to accommendate gramene QTL data
# 1. add gramene specific attrib_types in variationDB.attrib_type table
#	code	name	description
#	trait_category	trait category	category the trait belongs to
#	trait_symbol	trait symbol	symbol of this trait
#	publish_symbol	publish symbol	published symbol of this trait

use strict;
use Getopt::Long;
use DBI qw(:sql_types);
use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use ImportUtils;
use String::Approx qw(amatch adist);
use Algorithm::Diff qw(diff);
use XML::LibXML;
use Text::CSV;
use DB::Dumper;

# set output autoflush for progress bars
$| = 1;

my (
  $infile, $help,
  $host, $dbname, $user, $pass, $port,
  $chost, $cdbname, $cuser, $cpass, $cport,<commit_msg>add changes<commit_after>#!/usr/bin/env perl

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

# modified by <NAME> to accommendate gramene QTL data
# 1. add gramene specific attrib_types in variationDB.attrib_type table
#	code	name	description
#	trait_category	trait category	category the trait belongs to
#	trait_symbol	trait symbol	symbol of this trait
#	publish_symbol	publish symbol	published symbol of this trait

use strict;
use Getopt::Long;
use DBI qw(:sql_types);
use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use ImportUtils;
use String::Approx qw(amatch adist);
use Algorithm::Diff qw(diff);
use XML::LibXML;
use Text::CSV;
use Data::Dumper;

# set output autoflush for progress bars
$| = 1;

my (
  $infile, $help,
  $host, $dbname, $user, $pass, $port,
  $chost, $cdbname, $cuser, $cpass, $cport,
{'fraction_non_alphanumeric': 0.09072847682119205, 'fraction_numerical': 0.011920529801324504, 'mean_word_length': 5.115384615384615, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, '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': '4617740', 'n_tokens_mistral': 972, 'n_tokens_neox': 935, 'n_words': 368}