From 2bf1df17d32bdd74dcaa0e79301883495b674292 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 7 Oct 2004 16:42:24 +0000
Subject: [PATCH] xref sequence dumps are now configurable. See get_set_lists
method
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 259 ++++++++++++++----
1 file changed, 201 insertions(+), 58 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 558e414cab..2956ccbefe 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -33,36 +33,51 @@ Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
sub dump_seqs{
my ($self, $xref) = @_;
- $self->dump_ensembl();
$self->dump_xref($xref);
+ $self->dump_ensembl();
}
sub run_matching{
+ my ($self,$xref) = @_;
+
+ my @list=();
+
+ my $i = 0;
+ foreach my $method (@{$self->method()}){
+ my @dna=();
+ push @dna, $method;
+ push @dna, $xref->dir."/xref_".$i."_dna.fasta";
+ push @dna, $self->ensembl_dna_file();
+ push @list, \@dna;
+ my @pep=();
+ push @pep, $method;
+ push @pep, $xref->dir."/xref_".$i."_prot.fasta";
+ push @pep, $self->ensembl_protein_file();
+ push @list, \@pep;
+ $i++;
+ }
+
+ glenn_call(\@list);
print "NOT done yet:-)\n";
}
+
+sub glenn_call{
+ my ($lists) = @_;
+ foreach my $list (@$lists){
+ my ($meth, $q ,$t) = @$list;
+ print "HELLO: ".$meth."\n\t".$q."\n\t".$t."\n\n";
+ }
+}
+
sub store{
print "NOT done yet Either :-)\n";
}
-sub dump_xref{
- my ($self,$xref) = @_;
+sub get_species_id_from_species_name{
+ my ($xref,$species) = @_;
- if(!defined($xref->species())){
- $xref->species($self->species);
- }
- if(!defined($xref->dir())){
- if(defined($self->species)){
- $xref->species($self->species)
- }
- else{
- $xref->species(".");
- }
- }
- #
- # the species specified must be in the database and hence have a species_id
- #
- my $sql = "select species_id from species where name = '".$xref->species."'";
+ my $sql = "select species_id from species where name = '".$species."'";
my $dbi = $xref->dbi();
my $sth = $dbi->prepare($sql);
$sth->execute();
@@ -71,68 +86,188 @@ sub dump_xref{
if (defined @row) {
$species_id = $row[0];
} else {
- print STDERR "Couldn't get ID for species ".$xref->species."\n";
+ print STDERR "Couldn't get ID for species ".$species."\n";
print STDERR "It must be one of :-\n";
$sql = "select name from species";
- $sth = dbi()->prepare($sql);
+ $sth = $dbi->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
print STDERR $row[0]."\n";
}
- die("Please try again\n");
+ die("Please try again :-)\n");
}
+ return $species_id;
+}
- #
- # Dump out the sequences where the species has an id of species_id
- # and the sequence type is 'dna'
- #
- $self->xref_dna_file($xref->dir."/".$xref->species."_xref_dna.fasta");
- open(XDNA,">".$xref->dir."/".$xref->species."_xref_dna.fasta") || die "Could not open xref_dna.fasta";
- my $sql = "select p.xref_id, p.sequence from primary_xref p, xref x ";
- $sql .= "where p.xref_id = x.xref_id and ";
- $sql .= " p.sequence_type ='dna' and ";
- $sql .= " x.species_id = ".$species_id." ";
- $sth = $xref->dbi()->prepare($sql);
+
+sub get_set_lists{
+ my ($self) = @_;
+
+ return [["method1",["homo_sapiens","RefSeq"],["homo_sapiens","UniProtSwissProt"]],
+ ["method2",[$self->species,"*"]],
+ ["method3",["*","*"]]];
+}
+
+
+sub get_source_id_from_source_name{
+ my ($xref, $source) = @_;
+ my $source_id;
+
+ my $sql = "select source_id from source where name = '".$source."'";
+ my $dbi = $xref->dbi();
+ my $sth = $dbi->prepare($sql);
+ $sth->execute();
+ my @row = $sth->fetchrow_array();
+ if (defined $row[0] and $row[0] ne '') {
+ $source_id = $row[0];
+# print $source."\t*".$row[0]."*\n";
+ } else {
+ print STDERR "Couldn't get ID for source ".$source."\n";
+ print STDERR "It must be one of :-\n";
+ $sql = "select name from source";
+ $sth = $dbi->prepare($sql);
+ $sth->execute();
+ while(my @row = $sth->fetchrow_array()){
+ print STDERR $row[0]."\n";
+ }
+ die("Please try again :-)\n");
+ }
+ return $source_id;
+}
+
+sub dump_xref{
+ my ($self,$xref) = @_;
+
+ if(!defined($xref->dir())){
+ if(defined($self->dir)){
+ $xref->species($self->dir);
+ }
+ else{
+ $xref->dir(".");
+ }
+ }
+
+
+ my @method=();
+
+ my @lists =@{$self->get_set_lists()};
+
+ my $i=0;
+ foreach my $list (@lists){
+ print "method->".@$list[0]."\n";
+ $method[$i] = shift @$list;
+ my $j = 1;
+ my @source_id-();
+ my @species_id=();
+ foreach my $element (@$list){
+ while(my $species = shift(@$element)){
+ # print $j.")\t".$species."\n";
+ if($species ne "*"){
+ $species_id[$j] = get_species_id_from_species_name($xref,$species);
+ }
+ else{
+ $species_id[$j] = -1;
+ }
+ my $source = shift(@$element);
+ if($source ne "*"){
+ $source_id[$j] = get_source_id_from_source_name($xref,$source);
+ }
+ else{
+ $source_id[$j] = -1;
+ }
+ print $j."\t".$source. "\t".$source_id[$j] ."\n";
+ print $j."\t".$species."\t".$species_id[$j]."\n";
+ $j++;
+ }
+ }
+ #method data fully defined now
+ dump_subset($xref,\@species_id,\@source_id,$i);
+ $i++;
+ }
+
+ $self->method(\@method);
+
+ return;
+
+}
+
+
+sub dump_subset{
+ my ($xref,$rspecies_id,$rsource_id,$index) = @_;
+
+ open(XDNA,">".$xref->dir()."/xref_".$index."_dna.fasta")
+ || die "Could not open xref_".$index."_dna.fasta";
+
+ my $sql = "select p.xref_id, p.sequence, x.species_id , x.source_id ";
+ $sql .= " from primary_xref p, xref x ";
+ $sql .= " where p.xref_id = x.xref_id and ";
+ $sql .= " p.sequence_type ='dna' ";
+
+
+ for (my $j =1; $j<scalar(@$rspecies_id); $j++){
+ print $j."\t".$$rspecies_id[$j]."\t".$$rsource_id[$j]."\n";
+ }
+ # return $xref->dir."/xref_".$i."_dna.fasta";
+
+ my $sth = $xref->dbi()->prepare($sql);
$sth->execute();
my $i = 0;
while(my @row = $sth->fetchrow_array()){
- $i++;
- $row[1] =~ s/(.{60})/$1\n/g;
- print XDNA ">".$row[0]."\n".$row[1]."\n";
- if($i > 10){
- goto ENDDNA;
+ my $pass = 0;
+ for (my $j =1; $j<scalar(@$rspecies_id); $j++){
+ if($$rspecies_id[$j] < 0 or $row[2] == $$rspecies_id[$j]){
+ if($$rsource_id[$j] < 0 or $row[3] == $$rsource_id[$j]){
+ $pass = 1;
+ }
+ }
+ }
+ if($pass){
+ $i++;
+ $row[1] =~ s/(.{60})/$1\n/g;
+ print XDNA ">".$row[0]."\n".$row[1]."\n";
+ if($i > 10){
+ goto ENDDNA;
+ }
}
}
-ENDDNA:
+ ENDDNA:
close XDNA;
- #
- # Dump out the sequences where the species has an id of species_id
- # and the sequence type is 'peptide'
- #
- $self->xref_protein_file($xref->dir."/".$self->species."_xref_prot.fasta");
- open(XPEP,">".$xref->dir."/".$self->species."_xref_prot.fasta") || die "Could not open xref_prot.fasta";
- $sql = "select p.xref_id, p.sequence from primary_xref p, xref x ";
- $sql .= "where p.xref_id = x.xref_id and ";
- $sql .= " p.sequence_type ='peptide' and ";
- $sql .= " x.species_id = ".$species_id." ";
+
+ open(XPRO,">".$xref->dir."/xref_".$index."_prot.fasta")
+ || die "Could not open xref_".$index."_prot.fasta";
+ my $sql = "select p.xref_id, p.sequence, x.species_id , x.source_id ";
+ $sql .= " from primary_xref p, xref x ";
+ $sql .= " where p.xref_id = x.xref_id and ";
+ $sql .= " p.sequence_type ='peptide' ";
+
+
$sth = $xref->dbi()->prepare($sql);
$sth->execute();
$i = 0;
while(my @row = $sth->fetchrow_array()){
- $i++;
- $row[1] =~ s/(.{60})/$1\n/g;
- print XPEP ">".$row[0]."\n".$row[1]."\n";
- if($i > 10){
- goto ENDXPEP;
+ my $pass = 0;
+ for (my $j =1; $j<scalar(@$rspecies_id); $j++){
+ if($$rspecies_id[$j] < 0 or $row[2] == $$rspecies_id[$j]){
+ if($$rsource_id[$j] < 0 or $row[3] == $$rsource_id[$j]){
+ $pass = 1;
+ }
+ }
+ }
+ if($pass){
+ $i++;
+ $row[1] =~ s/(.{60})/$1\n/g;
+ print XPRO ">".$row[0]."\n".$row[1]."\n";
+ if($i > 10){
+ goto ENDPRO;
+ }
}
}
-ENDXPEP:
- close XPEP;
+ ENDPRO:
+ close XPRO;
}
-
sub dump_ensembl{
my ($self) = @_;
@@ -177,14 +312,14 @@ sub fetch_and_dump_seq{
foreach my $gene_id (@gene_ids){
$i++;
my $gene = $gene_adap->fetch_by_dbID($gene_id);
- print "gene ".$gene."\n";
+# print "gene ".$gene."\n";
foreach my $transcript (@{$gene->get_all_Transcripts()}) {
my $seq = $transcript->spliced_seq();
$seq =~ s/(.{60})/$1\n/g;
print DNA ">" . $transcript->dbID() . "\n" .$seq."\n";
my $trans = $transcript->translation();
my $translation = $transcript->translate();
- print "tranlation ".$translation."\n";
+# print "tranlation ".$translation."\n";
my $pep_seq = $translation->seq();
$pep_seq =~ s/(.{60})/$1\n/g;
print PEP ">".$trans->dbID()."\n".$pep_seq."\n";
@@ -236,6 +371,14 @@ sub ensembl_dna_file{
return $self->{_ens_dna_file};
}
+sub method{
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_method} = $arg );
+ return $self->{_method};
+}
+
#sub get_ensembl_type{
# my %type;
--
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