<commit_before>

use Test;
BEGIN { plan tests => 5 }



use lib './t';
use EnsTestDB;
use Bio::EnsEMBL::DBSQL::GenomicAlignAdaptor;
use Bio::AlignIO;

ok 1;

    
my $ens_test = EnsTestDB->new();

$ens_test->do_sql_file("t/genomicalign.dump");

my $db = $ens_test->get_DBSQL_Obj;

ok $ens_test;


$gadp = Bio::EnsEMBL::DBSQL::GenomicAlignAdaptor->new($db);

ok $gadp;

my $align = $gadp->fetch_GenomicAlign_by_dbID(1);

ok $align;

$alignblockset = $align->get_AlignBlockSet(1);

($a,$alignblock) = $alignblockset->get_AlignBlocks;

ok ($alignblock->start == 25 && $alignblock->end == 30 && $alignblock->align_start == 15 
	&& $alignblock->align_end == 20);

$alignout = Bio::AlignIO->new( -format => 'fasta',-fh => \*STDERR );

$alignout->write_aln($align);

<commit_msg>commented out AlignIO dumping from genomicalign.t<commit_after>

use Test;
BEGIN { plan tests => 5 }



use lib './t';
use EnsTestDB;
use Bio::EnsEMBL::DBSQL::GenomicAlignAdaptor;
#use Bio::AlignIO;

ok 1;

    
my $ens_test = EnsTestDB->new();

$ens_test->do_sql_file("t/genomicalign.dump");

my $db = $ens_test->get_DBSQL_Obj;

ok $ens_test;


$gadp = Bio::EnsEMBL::DBSQL::GenomicAlignAdaptor->new($db);

ok $gadp;

my $align = $gadp->fetch_GenomicAlign_by_dbID(1);

ok $align;

$alignblockset = $align->get_AlignBlockSet(1);

($a,$alignblock) = $alignblockset->get_AlignBlocks;

ok ($alignblock->start == 25 && $alignblock->end == 30 && $alignblock->align_start == 15 
	&& $alignblock->align_end == 20);

#$alignout = Bio::AlignIO->new( -format => 'fasta',-fh => \*STDERR );
#$alignout->write_aln($align);


{'fraction_non_alphanumeric': 0.19216182048040456, 'fraction_numerical': 0.015170670037926675, 'mean_word_length': 5.332, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 35, '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': '6925940', 'n_tokens_mistral': 690, 'n_tokens_neox': 647, 'n_words': 115}