<commit_before>#!/usr/local/ensembl/bin/perl -w

use strict;
use Getopt::Long;
use IO::File;
use File::Basename;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->no_version_check(1);

my $usage = "
Usage: $0 options

Options:
-host 
-dbname family dbname
-dbuser
-dbpass
-family_stable_id|-family_id
-mafft_file
-dir
-store

\n";

my ($family_stable_id,$starting_family_id,$starting_family_id_file,$num_families);

my $dir = ".";
my $store = 0;

my $mafft_executable = "/nfs/acari/avilella/src/mafft/mafft-6.522/scripts/mafft";
BEGIN {$ENV{MAFFT_BINARIES} = '/nfs/acari/avilella/src/mafft/mafft-6.522/binaries'; }

unless (-e $mafft_executable) {
  print STDERR "Error no binaries\n";
  exit 1;
}

my $help = 0;
my $host;
my $port = "";
my $dbname;
my $dbuser;
my $dbpass;
my $mafft_file;
my $fast = 0;
my $parttree = 0;

GetOptions('help' => \$help,
	   'h|host=s' => \$host,
	   'p|port=i' => \$port,
	   'db|dbname=s' => \$dbname,
	   'u|dbuser=s' => \$dbuser,
	   'ps|dbpass=s' => \$dbpass,
	   'fs|family_stable_id=s' => \$family_stable_id,<commit_msg>use system-wide compilation of mafft<commit_after>#!/usr/local/ensembl/bin/perl -w

use strict;
use Getopt::Long;
use IO::File;
use File::Basename;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->no_version_check(1);

my $usage = "
Usage: $0 options

Options:
-host 
-dbname family dbname
-dbuser
-dbpass
-family_stable_id|-family_id
-mafft_file
-dir
-store

\n";

my ($family_stable_id,$starting_family_id,$starting_family_id_file,$num_families);

my $dir = ".";
my $store = 0;

#my $mafft_executable = "/nfs/acari/avilella/src/mafft/mafft-6.522/scripts/mafft";
my $mafft_executable = "/software/ensembl/compara/mafft-6.522/bin/mafft";
BEGIN {$ENV{MAFFT_BINARIES} = '/software/ensembl/compara/mafft-6.522'; }

unless (-e $mafft_executable) {
  print STDERR "Error no binaries\n";
  exit 1;
}

my $help = 0;
my $host;
my $port = "";
my $dbname;
my $dbuser;
my $dbpass;
my $mafft_file;
my $fast = 0;
my $parttree = 0;

GetOptions('help' => \$help,
	   'h|host=s' => \$host,
	   'p|port=i' => \$port,
	   'db|dbname=s' => \$dbname,
	   'u|dbuser=s' => \$dbuser,
	   'ps|dbpass=s' => \$dbpass,
	   'fs|family_stable_id=s' => \$family_stable_id,
{'fraction_non_alphanumeric': 0.18981279930343928, 'fraction_numerical': 0.014801915542011318, 'mean_word_length': 4.618581907090465, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 19, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, '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': '6098186', 'n_tokens_mistral': 1088, 'n_tokens_neox': 1015, 'n_words': 186}