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olaaustine wants to merge 11 commits into from
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Adding check for population sets for variation sets script #1020

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d7431c1
Adding check for population sets
olaaustine Jul 26, 2023
c20f212
Adding the variation sets to the variation feature table
olaaustine Aug 2, 2023
f539bdd
Adding comments
olaaustine Aug 3, 2023
50e5881
Making changes based on review
olaaustine Aug 8, 2023
749652b
Adding the check for only dbsnp source
olaaustine Aug 8, 2023
f2018db
Chunking for variation sets
olaaustine Aug 18, 2023
0d007cc
Making final changes
olaaustine Aug 18, 2023
476f0e2
Changes after testing to the chunking process
olaaustine Aug 18, 2023
74691a9
Removing cut
olaaustine Aug 18, 2023
213e7b8
Fix for one var_set_id
olaaustine Aug 18, 2023
cf58c2b
removing the ignore
olaaustine Aug 18, 2023
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174 changes: 113 additions & 61 deletions scripts/import/dbSNP_v2/update_new_sets.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@
my $chunk = 1000000;
my $max_id = $vf->[0]->[1];


debug($config, "Dumping the variation sets and the new variation feature into files");
for my $tmp_num (map { $_ } $min_id/$chunk .. $max_id/$chunk) {
dump_old_sql_variation_sets($old_dbh, $tmp_num, $chunk, $max_id);
Expand All @@ -84,15 +85,15 @@
debug($config, "Loading new variation sets from merged file");
load_all_variation_sets($dbh, $tmp_merged);

debug($config, "Dumping new variation sets into a file to update the variation feature table");
for my $tmp_num (map { $_ } $min_id/$chunk .. $max_id/$chunk) {
dump_new_variation_sets($dbh, $tmp_num, $chunk, $max_id);
}

debug($config, "Updating the variation feature table");
update_variation_feature_table($dbh, $tmp_vs_file);
debug($config, "Recalculating the variation sets"); # takes from the merged file and recalculates and creates the concatenate file that will be used to update variation feature
recalculate($tmp_merged, $tmp_vs_file);


debug($config, "Updating the variation feature table");
for my $tmp_num (map { $_ } $min_id/$chunk .. $max_id/$chunk) {
update_variation_feature_table($dbh, $tmp_num, $chunk, $max_id);
}

debug($config, "Adding failed variation to variation set");
$dbh->do( qq{
Expand All @@ -106,6 +107,7 @@
}) or die "Failed to alter variation_set_variation keys";



sub temp_table {
my $dbhvar = shift;

Expand All @@ -124,9 +126,9 @@ sub create_merged_file {
my $new_vf_file = shift;
my $tmp_merged = shift;

open FILE1, "<", "$file" or die "Cannot open $file: $!";
open FILE2, "<", "$second_file" or die "Cannot open $second_file: $!";
open OUTPUT, ">", "$third_file" or die "Cannot open $third_file: $!";
open FILE1, "<", "$tmp_vset" or die "Cannot open $tmp_vset: $!";
open FILE2, "<", "$new_vf_file" or die "Cannot open $new_vf_file: $!";
open OUTPUT, ">", "$tmp_merged" or die "Cannot open $tmp_merged: $!";
my %data;

while (<FILE1>) {
Expand Down Expand Up @@ -165,72 +167,65 @@ sub load_all_variation_sets {
my $sql = qq{INSERT INTO variation_set_variation (variation_id, variation_set_id ) VALUES (?, ?)};
my $sth = $dbhvar->prepare($sql);

open FH, "<", "$load_file" or die "Can not open $load_file: $!";
while (<FH>) {
open my $load_vs, "<", "$load_file" or die "Can not open $load_file: $!";
while (<$load_vs>) {
chomp;
my $var_id = (split)[0];
my $var_set_id = (split)[1];

$sth->execute($var_id, $var_set_id);
}
close FH;
close $load_vs;
$sth->finish();

}

sub update_variation_feature_table {
# this function after populating the variation_feature_backup table created by inserting from the original table would then update the variation_set_id column uaing the file from the
# dump_new_variation_sets
my $dbhvar = shift;
my $load_file = shift;


my $update_temp_vf = $dbhvar->prepare(q{ UPDATE variation_feature SET variation_set_id = ?
WHERE variation_id = ? AND variation_set_id = ''});

#my %var_data;
open FH, "<", "$load_file" or die "Can not open $load_file: $!";
while (<FH>) {
chomp;
my $var_id = (split)[0];
my $var_set_id = (split)[1];
use Data::Dumper;
print Dumper($var_set_id, $var_id);

$update_temp_vf->execute($var_set_id, $var_id); # creating a hash which has the var_id has the key and the set var_set_id has the values
}

close FH;
$update_temp_vf->finish();
}


sub dump_new_variation_sets {
# this would dump the variation_sets table from the backup table and create a file vset_concat.txt with two columns which are var_id and sets of variation_set_id
my $dbhvar = shift;
# this function after populating the variation_feature_backup table created by inserting from the original table would then update the variation_set_id column uaing the file from the recalculate
# using the parents and parents set id to update the variation feature table
my $dbh = shift;
my $tmp_num = shift;
my $chunk = shift;
my $size = shift;

my $start = $chunk * $tmp_num;
my $end = $chunk + $start;
$end = $end < $size ? $end : $size;

my $dump_vs = $dbhvar->prepare(qq{ SELECT variation_id, GROUP_CONCAT(DISTINCT(variation_set_id)) FROM variation_set_variation WHERE variation_id > $start AND variation_id <= $end GROUP BY variation_id});
open (FH, ">>$TMP_DIR/$tmp_vs_file" )
or die( "Cannot open $TMP_DIR/$tmp_vs_file: $!" );
$dump_vs->execute();

while ( my $aref = $dump_vs->fetchrow_arrayref() ) {
my @a = map {defined($_) ? $_ : '\N'} @$aref;
print FH join("\t", @a), "\n";
my $update_sql = qq{ UPDATE variation_feature SET variation_set_id = ?
WHERE variation_id = ? AND variation_id > $start AND variation_id <= $end};

my $update_temp_vf = $dbh->prepare($update_sql);
#my %var_data;

open my $load_fh, "<", "$TMP_DIR/$tmp_vs_file" or die "Can not open $TMP_DIR/$tmp_vs_file`: $!";
while (<$load_fh>) {
chomp;
my @fields = split("\t");
my $var_id = $fields[0];
my $var_set_id = $fields[1];


my @sets_array;
my $values;
if ($var_set_id =~ /,/) {
my @sets_array = unique(split(',', $var_set_id));
my @sorted_array = sort { $a<=>$b } @sets_array;
$values = join(',', @sorted_array);
$values =~ s/\s*,\s*/,/g; # to eliminate spaces and stuff
$values =~ s/^\s+//; #to eliminate spaces and stuff
} else {
$values = "$var_set_id";
}

$update_temp_vf->execute($values, $var_id); # creating a hash which has the var_id has the key and the set var_set_id has the values
}

$dump_vs->finish();
close FH;
close $load_fh;
$update_temp_vf->finish();
}


sub dump_old_sql_variation_sets {
# this would dump old variation_sets table from the old database and create a file called variation_name_set.txt with two columns var_id and variation_set_id
my $dbhvar = shift;
Expand All @@ -244,22 +239,21 @@ sub dump_old_sql_variation_sets {


my $sql = qq{SELECT v.name, vs.variation_set_id from variation_set_variation vs LEFT JOIN variation v
ON v.variation_id = vs.variation_id where variation_set_id != 1 AND v.variation_id > $start AND v.variation_id <= $end };
ON v.variation_id = vs.variation_id where vs.variation_set_id != 1 AND v.source_id = 1 AND v.variation_id > $start AND v.variation_id <= $end };
my $sth = $dbhvar->prepare($sql);

local *FH;
open (FH, ">>$TMP_DIR/$tmp_vset" )
open (my $dump_fh, ">>$TMP_DIR/$tmp_vset" )
or die( "Cannot open $TMP_DIR/$tmp_vset: $!" );

$sth->execute();

while ( my $aref = $sth->fetchrow_arrayref() ) {
my @a = map {defined($_) ? $_ : '\N'} @$aref;
print FH join("\t", @a), "\n";
print $dump_fh join("\t", @a), "\n";
}

$sth->finish();
close FH;
close $dump_fh;

}

Expand All @@ -278,21 +272,79 @@ sub dump_new_variation_feature {
my $sql = qq{SELECT DISTINCT(variation_id), variation_name from variation_feature where variation_id > $start AND variation_id <= $end };
my $sth = $dbh->prepare($sql);

local *FH;
open (FH, ">>$TMP_DIR/$new_vf_file" )
open (my $dump_var, ">>$TMP_DIR/$new_vf_file" )
or die( "Cannot open $TMP_DIR/$new_vf_file: $!" );

$sth->execute();

while ( my $aref = $sth->fetchrow_arrayref() ) {
my @a = map {defined($_) ? $_ : '\N'} @$aref;
print FH join("\t", @a), "\n";
print $dump_var join("\t", @a), "\n";
}

$sth->finish();
close FH;
close $dump_var;


}

sub get_structure {
my $dbhvar = shift;

my $get_struc_sth = $dbhvar->prepare(qq[ select variation_set_sub, variation_set_super from variation_set_structure]);

my %parent;
$get_struc_sth->execute() ||die;
my $dat = $get_struc_sth->fetchall_arrayref();
foreach my $l(@{$dat}){
$parent{$l->[0]} = $l->[1] ;
}
return \%parent;

}

sub recalculate {
my $input_file = shift;
my $output_file = shift;

my $parent = get_structure($dbh);
my %concat_sets;

open my $re_input, "<", "$input_file" or die "Can not open $input_file: $!";


while (<$re_input>) {
chomp;
my @fields = split("\t");
my $var_id = $fields[0];
my $var_set_id = $fields[1];
my @sets;

push @{$concat_sets{$var_id}}, $var_set_id;
push @{$concat_sets{$var_id}}, $parent->{$var_set_id} if exists $parent->{$var_set_id}; #pushing parents and var_set_id
push @{$concat_sets{$var_id}}, $parent->{$parent->{$var_set_id}} if exists $parent->{$parent->{$var_set_id}};

}


open(my $re_output, '>', $output_file) or die "Could not open file '$output_file': $!";
foreach my $var_id (keys %concat_sets) {
my $values_str = join(", ", @{$concat_sets{$var_id}});
print $re_output "$var_id\t$values_str\n"; # adding the values str to it
}

# Close the file
close $re_output;
close $re_input;
}

sub unique {
my @array = shift;

my %u;
map { $u{$_} = 1; } @_;
return keys %u;

}

sub usage {
Expand Down