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Commit 0d3b1025 authored by Ian Longden's avatar Ian Longden
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renamed

parent b036ffb3
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Showing with 51 additions and 31 deletions
misc-scripts/assembly_patches/schema_patch_load.pl → misc-scripts/assembly_patches/assembly_patch_load.pl
View file @ 0d3b1025
......@@ -65,19 +65,22 @@ $sth->bind_columns(\$contig_coord_id) || die "What a bind NOT";
$sth->fetch() || die "Could not fetch coord_system_id";
$sth->finish;
my $get_code_sth = $dba->dbc->prepare("select attrib_type_id from attrib_type where code like ?");
my $get_seq_region_sth = $dba->dbc->prepare("select seq_region_id, length from seq_region where name like ?")
|| die "Could not prepare get_seq_region_sth";
my $get_seq_region_id_sth = $dba->dbc->prepare("select seq_region_id from seq_region where coord_system_id = ? and name like ?")
my $get_seq_region_id_sth = $dba->dbc->prepare("select seq_region_id, length from seq_region where coord_system_id = ? and name like ?")
|| die "Could not prepare get_seq_region_id_sth";
my $get_seq_id_sth = $dba->dbc->prepare("select sr.seq_region_id from seq_region sr , coord_system cs where sr.name like ? and cs.coord_system_id = sr.coord_system_id and cs.attrib like '%sequence%'");
my $insert_seq_region_sth = $dba->dbc->prepare("insert into seq_region (seq_region_id, name, coord_system_id, length) values(?, ?, ?, ?)") || die "Could not prepare seq_region insert sql";
#my $insert_seq_region_sth = $dba->dbc->prepare("insert into seq_region (seq_region_id, name, coord_system_id, length) values(?, ?, ?, ?)") || die "Could not prepare seq_region insert sql";
my $insert_dna_sth = $dba->dbc->prepare("insert into dna (seq_region_id, sequence) values (?, ?)")
|| die "Could not prepare insert dna sql";
#my $insert_dna_sth = $dba->dbc->prepare("insert into dna (seq_region_id, sequence) values (?, ?)")
# || die "Could not prepare insert dna sql";
#my $insert_attrib_sth = $dba->dbc->prepare("insert into seq_region_attrib (seq_region_id, attrib_type_id, value) values (?, ?, 1);";
my $coord_sth = $dba->dbc->prepare("select coord_system_id from coord_system where name like ? order by rank limit 1");
......@@ -85,17 +88,31 @@ if(!defined($chr_coord_id) or !defined($contig_coord_id)){
die "No coord_system_id for chromosome ($chr_coord_id) or contig ($contig_coord_id)\n";
}
my $non_ref;
my $toplevel;
$get_code_sth->execute("toplevel");
$get_code_sth->bind_columns(\$toplevel);
$get_code_sth->fetch;
$get_code_sth->execute("non_ref");
$get_code_sth->bind_columns(\$non_ref);
$get_code_sth->fetch;
# Store contigs as seq_region + dna.
#open(FASTA, "<".$fasta_file) || die "Could not open file $fasta_file";
open(MAPPER,"<".$mapping_file) || die "Could not open file $mapping_file";
open(TXT,"<".$txt_file) || die "Could not open file $txt_file";
open(SQL,">sql.txt") || die "Could not open sql.txt for writing\n";
my %acc_to_name;
my %txt_data;
my %key_to_index;
my %name_to_seq_id;
my %seq_id_to_start;
while(<TXT>){
if(/^#/){
......@@ -108,7 +125,7 @@ while(<TXT>){
}
foreach my $name (qw(alt_scaf_name alt_scaf_acc parent_type parent_name ori alt_scaf_start alt_scaf_stop parent_start parent_stop)){
if(!defined($key_to_index{$name})){
print "PROBLEM could not find index for $name\n";
print STDERR "PROBLEM could not find index for $name\n";
}
else{
print $name."\t".$key_to_index{$name}."\n";
......@@ -130,32 +147,41 @@ while(<TXT>){
die "COuld not get coord_system_id for ".$arr[$key_to_index{'parent_type'}];
}
my $seq_region_id;
my ($seq_region_id, $seq_length);
$get_seq_region_id_sth->execute($coord_sys, $arr[$key_to_index{'parent_name'}]);
$get_seq_region_id_sth->bind_columns(\$seq_region_id);
$get_seq_region_id_sth->bind_columns(\$seq_region_id,\$seq_length);
$get_seq_region_id_sth->fetch();
if(!defined($seq_region_id)){
die "COuld not get seq_region_id for ".$arr[$key_to_index{'parent_name'}]. " on coord system $coord_sys";
}
my $length = ($arr[$key_to_index{'alt_scaf_stop'}] - $arr[$key_to_index{'alt_scaf_start'}]) +1;
print "insert into seq_region (seq_region_id, name, coord_system_id, length)\n";
print "\tvalues ($max_seq_region_id, '$alt_name', $coord_sys, $length);\n\n";
# my $length = ($arr[$key_to_index{'alt_scaf_stop'}] - $arr[$key_to_index{'alt_scaf_start'}]) +1;
$name_to_seq_id{$alt_name} = $max_seq_region_id;
$name_to_seq_id{$alt_acc} = $max_seq_region_id;
$seq_id_to_start{$max_seq_region_id} = $arr[$key_to_index{'parent_start'}];
my $exc_len = $arr[$key_to_index{'parent_stop'}]-$arr[$key_to_index{'parent_start'}];
my $new_length = $arr[$key_to_index{'alt_scaf_stop'}]-$arr[$key_to_index{'alt_scaf_start'}];
print "insert into assembly_exception (assembly_exception_id, seq_region_id, seq_region_start, seq_region_end, exc_type, exc_seq_region_id, exc_seq_region_start, exc_seq_region_end, ori)\n";
print "\tvalues($max_assembly_exception_id, $max_seq_region_id, ",
$arr[$key_to_index{'alt_scaf_start'}], ",",
$arr[$key_to_index{'alt_scaf_stop'}], ",",
"'HAP',",
my $length = $seq_length + ($new_length-$exc_len);
print SQL "insert into seq_region (seq_region_id, name, coord_system_id, length)\n";
print SQL "\tvalues ($max_seq_region_id, '$alt_name', $coord_sys, $length);\n\n";
print SQL "insert into seq_region_attrib (seq_region_id, attrib_type_id, value) values ($max_seq_region_id, $toplevel, 1);\n";
print SQL "insert into seq_region_attrib (seq_region_id, attrib_type_id, value) values ($max_seq_region_id, $non_ref, 1);\n";
print SQL "insert into assembly_exception (assembly_exception_id, seq_region_id, seq_region_start, seq_region_end, exc_type, exc_seq_region_id, exc_seq_region_start, exc_seq_region_end, ori)\n";
print SQL "\tvalues($max_assembly_exception_id, $max_seq_region_id, ",
($arr[$key_to_index{'alt_scaf_start'}]+$arr[$key_to_index{'parent_start'}])-1, ",",
($arr[$key_to_index{'alt_scaf_stop'}]+$arr[$key_to_index{'parent_start'}])-1, ",",
# ($new_length+$arr[$key_to_index{'parent_start'}], ",",
"'HAP', ",
$seq_region_id,", ",
$arr[$key_to_index{'parent_start'}], ",",
$arr[$key_to_index{'parent_start'}], ", ",
$arr[$key_to_index{'parent_stop'}], ",",
" 1)\n\n";
" 1);\n\n";
$max_seq_region_id++;
$max_assembly_exception_id++;
......@@ -254,24 +280,16 @@ while(<MAPPER>){
if(!defined($cmp_seq_id)){
die "Could not get seq id for $contig\n\n";
}
print "insert into assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start , cmp_end, ori) \n";
print " values(".$name_to_seq_id{$acc}.", ".$cmp_seq_id.", $p_start, $p_end, $c_start, $c_end, $strand)\n\n";
my $seq_id = $name_to_seq_id{$acc};
print SQL "insert into assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start , cmp_end, ori) \n";
print SQL " values(".$seq_id.", ".$cmp_seq_id.", ".(($seq_id_to_start{$seq_id}+$p_start)-1).", ".(($seq_id_to_start{$seq_id}+$p_end)-1).", $c_start, $c_end, $strand);\n\n";
}
else{
print "GAP of $contig length\n";
}
}
# add mappings
# First the ref -> haplotype mappings
# Then haplo -> contig mappings
# create haplotype in assembly_exception
#Do these things just have names or versions too?
close SQL;
sub load_seq_region{
......@@ -296,8 +314,10 @@ sub load_seq_region{
}
print "adding new seq region $name length of sequence = ".length($$seq)."\n";
print SQL "insert into seq_region (seq_region_id, name, coord_system_id, length) values ($max_seq_region_id, '$name', $contig_coord_id, ".length($$seq).");\n";
# $insert_seq_region_sth->execute($max_seq_region_id, $name, $contig_coord_id, length($$seq))
# || die "Could not insert seq region for $name";
print SQL "insert into dna (seq_region_id, sequence) values ($max_seq_region_id,'".$$seq."');\n\n";
# $insert_dna_sth->execute($max_seq_region_id, $seq)
# || die "Could not add seq for $name";
......
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