| Bio-Das documentation | Contained in the Bio-Das distribution. |
Tony Cox <avc@sanger.ac.uk>.
Copyright (c) 2003 The Sanger Institute
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
| Bio-Das documentation | Contained in the Bio-Das distribution. |
package Bio::Das::AGPServer::SQLStorage::CSV::DB;
use strict; use Bio::Das::AGPServer::Parser; use vars qw($AUTOLOAD $DEBUG @ISA); $Bio::Das::AGPServer::SQLStorage::CSV::DB::DEBUG = 1; @ISA = ("Bio::Das::AGPServer::SQLStorage"); sub new { my ($class, $config) = @_; my $o = bless {}, $class; $o->init($config); return $o; } ################################################################# ## Init the options object ################################################################# sub init { my ($self,$config) = @_; $self->config($config); my $tablename = $config->tablename(); my $tmpdir = $config->tmpdir(); if (-e "$tmpdir/$tablename"){ unlink("$tmpdir/$tablename"); print STDERR "Removed $tmpdir/$tablename\n" if ($Bio::Das::AGPServer::SQLStorage::CSV::DB::DEBUG == 1); } my $dbh = DBI->connect("DBI:CSV:f_dir=$tmpdir") or die $DBI::errstr; $self->db_handle($dbh); $dbh->{'csv_tables'}->{$tablename} = { 'col_names' => [ "chr", "chr_start", "chr_end", "ord","type", "embl_id", "embl_start", "embl_end", "embl_ori" ] }; $self->create_agp_table(); # done by base class if ($config->agpdir()){ my $dir = $config->agpdir(); opendir(DIR, "$dir") or die "Cannot open AGP directory: $!\n"; my @agpfiles = grep /.*\.agp$/i, readdir DIR; foreach my $file (@agpfiles){ print STDERR "Loading AGP data file: $file\n" if ($Bio::Das::AGPServer::SQLStorage::CSV::DB::DEBUG == 1); my $parser = Bio::Das::AGPServer::Parser->new("$dir/$file"); $self->load_agp($parser); # done by base class } } elsif ($config->agpfile()) { print STDERR "Loading AGP data file: ", $config->agpfile(), "\n" if ($Bio::Das::AGPServer::SQLStorage::CSV::DB::DEBUG == 1); my $parser = Bio::Das::AGPServer::Parser->new($config->agpfile()); $self->load_agp($parser); # done by base class } else { die "Cannot parse AGP data!\n"; } } ######################################################################################## sub entry_points { my ($self) = @_; my $dbh = $self->db_handle(); my $host = $self->config->hostname(); my $port = $self->config->port(); my $dsn = $self->config->dsn(); my $table = $self->config->tablename(); my $content .= $self->open_dasep(); my $query = qq(SELECT DISTINCT chr from $table); my $sth = $dbh->prepare($query); $sth->execute(); my %CHR = (); while (my $row = $sth->fetchrow_hashref()){ $CHR{$row->{'chr'}} = 0; } foreach my $key (keys %CHR){ next if ($key =~ /CHR/); # skip first row of table (column names) my $query = qq(SELECT MAX(chr_end) from $table where chr = '$key'); my $sth = $dbh->prepare($query); $sth->execute(); while (my ($length) = $sth->fetchrow_array()){ $content .= qq( <SEGMENT id="$key" size="$length" subparts="yes" />\n); } } $content .= $self->close_dasep(); return ($content); } ################################################################# sub feature_by_id { my ($self,$feature_list) = @_; my $dbh = $self->db_handle(); my $table = $self->config->tablename(); my $dsn = $self->config->dsn(); my $host = $self->config->hostname(); my $port = $self->config->port(); my $response = ""; foreach my $feature (@{$feature_list}){ my $query = qq(SELECT type,chr,embl_id,embl_start,embl_end,chr_start,chr_end,embl_ori from $table where embl_id LIKE '%$feature%'); my $sth = $dbh->prepare($query); $sth->execute(); while( my ($type,$chr,$eid,$es,$ee,$cs,$ce,$eo) = $sth->fetchrow_array()){ my $status = "clone_status:$type:" . $Bio::Das::AGPServer::SQLStorage::CLONE_STATUS->{$type}; $response .= qq( <SEGMENT id="$chr" version="1" start="$cs" stop="$ce">\n); $response .= qq( <FEATURE id="components/$eid" label="components/$eid">\n); $response .= qq( <TYPE id="static_golden_path" reference="yes" subparts="no">static_golden_path</TYPE>\n); $response .= qq( <METHOD id="agp-clone">agp-clone</METHOD>\n); $response .= qq( <START>$cs</START>\n); $response .= qq( <END>$ce</END>\n); $response .= qq( <SCORE>-</SCORE>\n); $response .= qq( <ORIENTATION>$eo</ORIENTATION>\n); $response .= qq( <PHASE>-</PHASE>\n); $response .= qq( <NOTE>$status</NOTE>\n); $response .= qq( <TARGET id="$eid" start="$es" stop="$ee" />\n); $response .= qq( </FEATURE>\n); $response .= qq( </SEGMENT>\n); } } return($response); } ################################################################# sub features { my ($self,$segment_list) = @_; my $dbh = $self->db_handle(); my $table = $self->config->tablename(); my $dsn = $self->config->dsn(); my $host = $self->config->hostname(); my $port = $self->config->port(); my $response = ""; my $query = qq(SELECT * from $table where chr = ? AND chr_start < ? AND chr_end > ? ORDER by chr_start); my $sth = $dbh->prepare($query); foreach my $segment(@{$segment_list}){ my ($chr,$rest) = split(":",$segment); my ($start,$end) = split(",",$rest); $response .= qq( <SEGMENT id="$chr" version="1" start="$start" stop="$end">\n); $sth->execute($chr,$end,$start); while (my $row = $sth->fetchrow_hashref()){ my $type = $row->{'type'}; my $id = $row->{'embl_id'}; my $es = $row->{'embl_start'}; my $ee = $row->{'embl_end'}; my $cs = $row->{'chr_start'}; my $ce = $row->{'chr_end'}; my $eo = $row->{'embl_ori'}; my $status = "clone_status:$type:" . $Bio::Das::AGPServer::SQLStorage::CLONE_STATUS->{$type}; $response .= qq( <FEATURE id="components/$id" label="components/$id">\n); $response .= qq( <TYPE id="static_golden_path" reference="yes" subparts="no">static_golden_path</TYPE>\n); $response .= qq( <METHOD id="agp-clone">agp-clone</METHOD>\n); $response .= qq( <START>$cs</START>\n); $response .= qq( <END>$ce</END>\n); $response .= qq( <SCORE>-</SCORE>\n); $response .= qq( <ORIENTATION>$eo</ORIENTATION>\n); $response .= qq( <PHASE>-</PHASE>\n); $response .= qq( <NOTE>$status</NOTE>\n); $response .= qq( <TARGET id="$id" start="$es" stop="$ee" />\n); $response .= qq( </FEATURE>\n); } $response .= " </SEGMENT>\n"; } $sth->finish(); return($response); } 1;