From c70d4ffb697148bbfe9273fc05b513f4fd4a8dcf Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Mon, 11 Oct 2004 16:02:48 +0000
Subject: [PATCH] Removed - functionality now in BasicMapper.pm
---
misc-scripts/xref_mapping/ensembl_dumper.pl | 38 --
.../xref_mapping/exonerate_prototype.pl | 399 ------------------
misc-scripts/xref_mapping/xref_dumper.pl | 34 --
3 files changed, 471 deletions(-)
delete mode 100644 misc-scripts/xref_mapping/ensembl_dumper.pl
delete mode 100644 misc-scripts/xref_mapping/exonerate_prototype.pl
delete mode 100644 misc-scripts/xref_mapping/xref_dumper.pl
diff --git a/misc-scripts/xref_mapping/ensembl_dumper.pl b/misc-scripts/xref_mapping/ensembl_dumper.pl
deleted file mode 100644
index 42098df35d..0000000000
--- a/misc-scripts/xref_mapping/ensembl_dumper.pl
+++ /dev/null
@@ -1,38 +0,0 @@
-# Dump Ensembl sequences to fasta file
-
-use strict;
-
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-
-my $host = 'ecs2';
-my $port = 3364;
-my $user = 'ensro';
-my $dbname = 'homo_sapiens_core_25_34e';
-
-my $file = "ensembl_transcripts.fasta";
-
-my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
- -port => $port,
- -user => $user,
- -dbname => $dbname);
-
-my $slice_adaptor = $db->get_SliceAdaptor();
-my $slice = $slice_adaptor->fetch_by_region('chromosome', '21');
-
-my $t = 0;
-
-open(FILE, ">" . $file);
-
-foreach my $gene (@{$slice->get_all_Genes()}) {
-
- foreach my $trans (@{$gene->get_all_Transcripts()}) {
-
- print FILE ">" . $trans->dbID() . "\n" . $trans->spliced_seq() . "\n";
- $t++;
-
- }
-}
-
-close(FILE);
-
-print "Wrote $t transcripts to $file\n";
diff --git a/misc-scripts/xref_mapping/exonerate_prototype.pl b/misc-scripts/xref_mapping/exonerate_prototype.pl
deleted file mode 100644
index f19c6ee78a..0000000000
--- a/misc-scripts/xref_mapping/exonerate_prototype.pl
+++ /dev/null
@@ -1,399 +0,0 @@
-use strict;
-
-use DBI;
-use File::Basename;
-use IPC::Open3;
-
-# Use exonerate (or other program) to find xref-ensembl obejct mappings
-
-
-# XXX
-my $queryfile = "xref_dna.fasta";
-my $targetfile = "ensembl_transcripts.fasta";
-
-run_mapping($queryfile, $targetfile, ".");
-store($targetfile);
-
-sub run_mapping {
-
- my ($queryfile, $targetfile, $root_dir) = @_;
-
- # get list of methods
- my @methods = ("ExonerateBest1"); # TODO get from Ian, maybe files as well
-
- # foreach method, submit the appropriate job & keep track of the job name
- my @job_names;
-
- foreach my $method (@methods) {
-
- my $obj_name = "XrefMapper::Methods::$method";
- # check that the appropriate object exists
- eval "require $obj_name";
- if($@) {
-
- warn("Could not find object $obj_name corresponding to mapping method $method, skipping\n$@");
-
- } else {
-
- my $obj = $obj_name->new();
- my $job_name = $obj->run($queryfile, $targetfile);
- push @job_names, $job_name;
- print "Submitted LSF job $job_name to list\n";
- sleep 1; # make sure unique names really are unique
-
- }
-
- } # foreach method
-
- # submit depend job to wait for all mapping jobs
- submit_depend_job($root_dir, @job_names);
-
-
-} # run_exonerate
-
-
-sub submit_depend_job {
-
- my ($root_dir, @job_names) = @_;
-
- # Submit a job that does nothing but wait on the main jobs to
- # finish. This job is submitted interactively so the exec does not
- # return until everything is finished.
-
- # build up the bsub command; first part
- my @depend_bsub = ('bsub', '-K');
-
- # one -wended clause for each main job
- foreach my $job (@job_names) {
- push @depend_bsub, "-wended($job)";
- }
-
- # rest of command
- push @depend_bsub, ('-q', 'small', '-o', "$root_dir/depend.out", '-e', "$root_dir/depend.err", '/bin/true');
-
- #print "depend bsub:\n" . join (" ", @depend_bsub) . "\n";
-
- my ($depend_wtr, $depend_rtr, $depend_etr, $depend_pid);
- $depend_pid = open3($depend_wtr, $depend_rtr, $depend_etr, @depend_bsub);
- my $depend_jobid;
- while (<$depend_rtr>) {
- if (/Job <([0-9]+)> is/) {
- $depend_jobid = $1;
- print "LSF job ID for depend job: $depend_jobid \n" ;
- }
- }
- if (!defined($depend_jobid)) {
- print STDERR "Error: could not get depend job ID\n";
- }
-
-
-
-}
-
-=head2 store
-
- Arg[1] : The target file used in the exonerate run. Used to work out the Ensembl object type.
- Arg[2] :
- Example : none
- Description: Parse exonerate output files and build files for loading into target db tables.
- Returntype : List of strings
- Exceptions : none
- Caller : general
-
-=cut
-
-sub store {
-
- my ($target_file_name) = @_;
-
- my $type = get_ensembl_object_type($target_file_name);
-
- # get or create the appropriate analysis ID
- my $analysis_id = get_analysis_id($type);
-
- # TODO - get this from config
- my $dbi = DBI->connect("dbi:mysql:host=ecs1g;port=3306;database=arne_core_20_34",
- "ensadmin",
- "ensembl",
- {'RaiseError' => 1}) || die "Can't connect to database";
-
- # get current max object_xref_id
- my $max_object_xref_id = 0;
- my $sth = $dbi->prepare("SELECT MAX(object_xref_id) FROM object_xref");
- $sth->execute();
- my $max_object_xref_id = ($sth->fetchrow_array())[0];
- if (!defined $max_object_xref_id) {
- print "Can't get highest existing object_xref_id, using 1\n)";
- } else {
- print "Maximum existing object_xref_id = $max_object_xref_id\n";
- }
-
-
- #my $ox_sth = $dbi->prepare("INSERT INTO object_xref(ensembl_id, ensembl_object_type, xref_id) VALUES(?,?,?)");
-
- #my $ix_sth = $dbi->prepare("INSERT INTO identity_xref VALUES(?,?,?,?,?,?,?,?,?,?,?)");
-
- # files to write table data to
- open (OBJECT_XREF, ">object_xref.txt");
- open (IDENTITY_XREF, ">identity_xref.txt");
-
- my $total_lines = 0;
- my $total_files = 0;
-
- my $object_xref_id = $max_object_xref_id + 1;
-
- # keep a (unique) list of xref IDs that need to be written out to file as well
- my %primary_xref_ids;
-
- foreach my $file (glob("*.map")) {
-
- print "Parsing results from $file \n";
- open(FILE, $file);
- $total_files++;
-
- while (<FILE>) {
-
- $total_lines++;
- chomp();
- my ($label, $query_id, $target_id, $query_start, $query_end, $target_start, $target_end, $cigar_line, $score) = split(/:/, $_);
- $cigar_line =~ s/ //;
-
- # TODO make sure query & target are the right way around
-
- print OBJECT_XREF "$object_xref_id\t$target_id\t$type\t$query_id\n";
- print IDENTITY_XREF "$object_xref_id\t$query_id\t$target_id\t$query_start\t$query_end\t$target_start\t$target_end\t$cigar_line\t$score\t\\N\t$analysis_id\n";
- # TODO - evalue?
- $object_xref_id++;
-
- $primary_xref_ids{$query_id} = $query_id;
-
- # Store in database
- # create entry in object_xref and get its object_xref_id
- #$ox_sth->execute($target_id, $type, $query_id) || warn "Error writing to object_xref table";
- #my $object_xref_id = $ox_sth->{'mysql_insertid'};
-
- # create entry in identity_xref
- #$ix_sth->execute($object_xref_id, $query_id, $target_id, $query_start, $query_end, $target_start, $target_end, $cigar_line, $score, undef, $analysis_id) || warn "Error writing to identity_xref table";
-
- }
-
- close(FILE);
-
- }
-
- close(IDENTITY_XREF);
- close(OBJECT_XREF);
-
- print "Read $total_lines lines from $total_files exonerate output files\n";
-
- # write relevant xrefs to file
- dump_xrefs(\%primary_xref_ids);
-
-}
-
-
-sub get_ensembl_object_type {
-
- my $filename = shift;
- my $type;
-
- if ($filename =~ /gene/i) {
-
- $type = "Gene";
-
- } elsif ($filename =~ /transcript/i) {
-
- $type = "Transcript";
-
- } elsif ($filename =~ /translation/i) {
-
- $type = "Translation";
-
- } else {
-
- print STDERR "Cannot deduce Ensembl object type from filename $filename";
- }
-
- return $type;
-
-}
-
-
-sub get_analysis_id {
-
- my $ensembl_type = shift;
-
- my %typeToLogicName = ( 'transcript' => 'XrefExonerateDNA',
- 'translation' => 'XrefExonerateProtein' );
-
- my $logic_name = $typeToLogicName{lc($ensembl_type)};
-
- # TODO - get these details from Config
- my $host = "ecs1g";
- my $port = 3306;
- my $database = "arne_core_20_34";
- my $user = "ensadmin";
- my $password = "ensembl";
-
- my $dbi = DBI->connect("dbi:mysql:host=$host;port=$port;database=$database",
- "$user",
- "$password",
- {'RaiseError' => 1}) || die "Can't connect to database";
-
-
- my $sth = $dbi->prepare("SELECT analysis_id FROM analysis WHERE logic_name='" . $logic_name ."'");
- $sth->execute();
-
- my $analysis_id;
-
- if (my @row = $sth->fetchrow_array()) {
-
- $analysis_id = $row[0];
- print "Found exising analysis ID ($analysis_id) for $logic_name\n";
-
- } else {
-
- print "No analysis with logic_name $logic_name found, creating ...\n";
- $sth = $dbi->prepare("INSERT INTO analysis (logic_name, created) VALUES ('" . $logic_name. "', NOW())");
- # TODO - other fields in analysis table
- $sth->execute();
- $analysis_id = $sth->{'mysql_insertid'};
- print "Done (analysis ID=" . $analysis_id. ")\n";
-
- }
-
- return $analysis_id;
-
-}
-
-
-sub dump_xrefs {
-
- my $xref_ids_hashref = shift;
- my @xref_ids = keys %$xref_ids_hashref;
-
- open (XREF, ">xref.txt");
-
- # TODO - get this from config
- my $xref_dbi = DBI->connect("dbi:mysql:host=ecs1g;port=3306;database=glenn_test_xref",
- "ensro",
- "",
- {'RaiseError' => 1}) || die "Can't connect to database";
-
- my $core_dbi = DBI->connect("dbi:mysql:host=ecs1g;port=3306;database=arne_core_20_34",
- "ensro",
- "",
- {'RaiseError' => 1}) || die "Can't connect to database";
-
- # get current highest internal ID from xref
- my $max_xref_id = 0;
- my $core_sth = $core_dbi->prepare("SELECT MAX(xref_id) FROM xref");
- $core_sth->execute();
- my $max_xref_id = ($core_sth->fetchrow_array())[0];
- if (!defined $max_xref_id) {
- print "Can't get highest existing xref_id, using 0\n)";
- } else {
- print "Maximum existing xref_id = $max_xref_id\n";
- }
- my $core_xref_id = $max_xref_id + 1;
-
- # keep a unique list of source IDs to build the external_db table later
- my %source_ids;
-
- # execute several queries with a max of 200 entries in each IN clause - more efficient
- my $batch_size = 200;
-
- while(@xref_ids) {
-
- my @ids;
- if($#xref_ids > $batch_size) {
- @ids = splice(@xref_ids, 0, $batch_size);
- } else {
- @ids = splice(@xref_ids, 0);
- }
-
- my $id_str;
- if(@ids > 1) {
- $id_str = "IN (" . join(',', @ids). ")";
- } else {
- $id_str = "= " . $ids[0];
- }
-
-
- my $sql = "SELECT * FROM xref WHERE xref_id $id_str";
- my $xref_sth = $xref_dbi->prepare($sql);
- $xref_sth->execute();
-
- my ($xref_id, $accession, $label, $description, $source_id, $species_id);
- $xref_sth->bind_columns(\$xref_id, \$accession, \$label, \$description, \$source_id, \$species_id);
-
- # note the xref_id we write to the file is NOT the one we've just read
- # from the internal xref database as the ID may already exist in the core database
- while (my @row = $xref_sth->fetchrow_array()) {
- print XREF "$core_xref_id\t$accession\t$label\t$description\n";
- $source_ids{$source_id} = $source_id;
- $core_xref_id++;
- if ($source_id == 1001) {
- print "xref $xref_id has source_id 1001\n";
- }
- }
-
- # Now get the dependent xrefs for each of these xrefs and write them as well
- $sql = "SELECT x.accession, x.label, x.description, x.source_id FROM dependent_xref dx, xref x WHERE x.xref_id=dx.master_xref_id AND master_xref_id $id_str";
- my $dep_sth = $xref_dbi->prepare($sql);
- $dep_sth->execute();
-
- $dep_sth->bind_columns(\$accession, \$label, \$description, \$source_id);
- while (my @row = $dep_sth->fetchrow_array()) {
- print XREF "$core_xref_id\t$accession\t$label\t$description\tDEPENDENT\n";
- $source_ids{$source_id} = $source_id;
- $core_xref_id++;
- }
- #print "source_ids: " . join(" ", keys(%source_ids)) . "\n";
-
- } # while @xref_ids
-
- close(XREF);
-
- # now write the exernal_db file - the %source_ids hash will contain the IDs of the
- # sources that need to be written as external_dbs
- open(EXTERNAL_DB, ">external_db.txt");
-
- # get current highest internal ID from external_db
- my $max_edb_id = 0;
- my $core_sth = $core_dbi->prepare("SELECT MAX(external_db_id) FROM external_db");
- $core_sth->execute();
- my $max_edb_id = ($core_sth->fetchrow_array())[0];
- if (!defined $max_edb_id) {
- print "Can't get highest existing external_db_id, using 0\n)";
- } else {
- print "Maximum existing external_db_id = $max_edb_id\n";
- }
- my $edb_id = $max_edb_id + 1;
-
- my @source_id_array = keys %source_ids;
- my $source_id_str;
- if(@source_id_array > 1) {
- $source_id_str = "IN (" . join(',', @source_id_array). ")";
- } else {
- $source_id_str = "= " . $source_id_array[0];
- }
-
- my $source_sql = "SELECT name, release FROM source WHERE source_id $source_id_str";
- my $source_sth = $xref_dbi->prepare($source_sql);
- $source_sth->execute();
-
- my ($source_name, $release);
- $source_sth->bind_columns(\$source_name, \$release);
-
- while (my @row = $source_sth->fetchrow_array()) {
- print EXTERNAL_DB "$edb_id\t$source_name\t$release\tXREF\n";
- # TODO knownxref etc??
- $edb_id++;
- }
-
- close(EXTERNAL_DB);
-
-
-
-}
diff --git a/misc-scripts/xref_mapping/xref_dumper.pl b/misc-scripts/xref_mapping/xref_dumper.pl
deleted file mode 100644
index af6c7cd63d..0000000000
--- a/misc-scripts/xref_mapping/xref_dumper.pl
+++ /dev/null
@@ -1,34 +0,0 @@
-# Dump primary xrefs to FASTA file
-
-use strict;
-use DBI;
-
-my $file = "xref_dna.fasta";
-
-my $host = "ecs1g";
-my $port = 3306;
-my $database = "glenn_test_xref";
-my $user = "ensadmin";
-my $password = "ensembl";
-
-my $dbi = DBI->connect("dbi:mysql:host=$host;port=$port;database=$database",
- "$user",
- "$password",
- {'RaiseError' => 1}) || die "Can't connect to database";
-
-open(FILE, ">" . $file);
-
-my $sth = $dbi->prepare("SELECT x.xref_id, px.sequence FROM primary_xref px, source so, xref x, species sp WHERE sp.name='homo_sapiens' AND so.name='RefSeq' AND x.species_id=sp.species_id AND px.source_id=so.source_id AND x.xref_id=px.xref_id AND px.sequence_type='dna' LIMIT 500");
-$sth->execute();
-
-my ($xref_id, $sequence);
-$sth->bind_columns(\$xref_id, \$sequence);
-
-while (my @row = $sth->fetchrow_array()) {
-
- print FILE ">$xref_id\n$sequence\n";
-
-}
-
-close(FILE);
-
--
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