From b0ef93bb713c134b66be14fdbe0baed692e8fa61 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 20 Dec 2002 16:47:45 +0000
Subject: [PATCH] removal of no longer needed EMBL loading
---
.../embl_annotation/extract_curated.pl | 399 ------------------
1 file changed, 399 deletions(-)
delete mode 100755 misc-scripts/embl_annotation/extract_curated.pl
diff --git a/misc-scripts/embl_annotation/extract_curated.pl b/misc-scripts/embl_annotation/extract_curated.pl
deleted file mode 100755
index 99860c25f7..0000000000
--- a/misc-scripts/embl_annotation/extract_curated.pl
+++ /dev/null
@@ -1,399 +0,0 @@
-#!/usr/local/bin/perl
-
-# script to extract annotation from EMBL files and insert it into an
-# ensembl database
-
-use strict;
-
-use Getopt::Long;
-
-use Bio::EnsEMBL::EMBLLOAD::Obj;
-use Bio::EnsEMBL::DBLoader;
-use Bio::SeqIO;
-use Bio::EnsEMBL::DBSQL::DBEntryAdaptor;
-
-# embl genes will be written to this database:
-my $ohost='localhost';
-my $ouser='root';
-my $odbname='embl_test';
-my $pass='';
-
-# list of clones in ensembl for which an embl file should be
-# checked is read from here
-my $ihost='localhost';
-my $iuser='root';
-my $idbname='';
-
-# test file
-my $emblfile='AL109928.embl';
-my $write;
-my $verbose;
-my $list;
-my $delete;
-my $clone_id;
-my $processed_clone_list='extract_curated.processed.lis';
-my $log='extract_curated.log.err';
-my $max_clone;
-my $nodb;
-my $help;
-&GetOptions(
-
- 'ohost:s'=>\$ohost,
- 'ouser:s'=>\$ouser,
- 'odbname:s'=>\$odbname,
-
- 'ihost:s'=>\$ihost,
- 'iuser:s'=>\$iuser,
- 'idbname:s'=>\$idbname,
-
- 'emblfile:s'=>\$emblfile,
-
- 'w'=>\$write,
- 'v'=>\$verbose,
- 'l'=>\$list,
- 'd'=>\$delete,
- 'c:s'=>\$clone_id,
- 'log:s'=>\$log,
- 'processed:s'=>\$processed_clone_list,
- 'max:n'=>\$max_clone,
- 'nodb'=>\$nodb,
- 'help|h'=>\$help,
- );
-
-if($help){
- print << "ENDOFTEXT";
-extract_curated.pl
-
- -v verbose
- -w write gene structures to output database
-
- -d delete (used with mode 2 to remove entries from database - bugs)
- -c clone_id clone_id override (to replace id read from embl file by id that will be
- used to name genes and write to database)
-
- -log file log file for stack trace of fatal errors (mode 1) [$log]
- -processed file file of all previously processed clones that have not been written to
- database - read before and written after processing (mode 1)
- -max number number of clones to process (mode 1)
- -nodb allow script to run without presence of database (testing only)
-
-Two sources of data to process:
- -l select list mode (mode 1)
-
-1. process all entries in 'clone' table of input database that are not
- present in corresponding table of output database or in 'processed' log file.
- -ihost hostname hostname of input database [$ihost]
- -iuser username username of input database [$iuser]
- -idbname dbname name of input database [$idbname]
-
-2. read a single file:
- -emblfile file specify file for processing [$emblfile]
-
-
- -ohost hostname hostname of input database [$ohost]
- -ouser username username of input database [$ouser]
- -odbname dbname name of input database [$odbname]
-
- -h help
-ENDOFTEXT
- exit;
-}
-
-# use -d -c clone to force a delete
-
-my $nunfin=0;
-my $nnoembl=0;
-my $nwrongsv=0;
-my $nclonefail=0;
-my $nclonenogene=0;
-my $nclonegene=0;
-my $ngeneok=0;
-
-my %processed;
-my $logging;
-
-my $gene_map_file=">txt/gene_stable_id.txt";
-my $transcript_map_file=">txt/transcript_stable_id.txt";
-my $exon_map_file=">txt/exon_stable_id.txt";
-my $translation_map_file=">txt/translation_stable_id.txt";
-
-system("mkdir txt");
-open(GENE_MAP,$gene_map_file) || die "cant open $gene_map_file";
-open(TRANSCRIPT_MAP,$transcript_map_file) || die "cant open $transcript_map_file";
-open(EXON_MAP,$exon_map_file) || die "cant open $exon_map_file";
-open(TRANSLATION_MAP,$translation_map_file) || die "cant open $translation_map_file";
-
-# connect to db for writing
-my $db;
-my $adx;
-unless($nodb){
- $db = Bio::EnsEMBL::DBLoader->new(
- "Bio::EnsEMBL::DBSQL::DBAdaptor/host=$ohost;user=$ouser;dbname=$odbname;pass=$pass");
- # adaptor for xrefs
- $adx = Bio::EnsEMBL::DBSQL::DBEntryAdaptor->new($db);
-}
-
-my $dbi;
-if($list){
-
- # open log
- if($write){
- open(LOG,">$log") || die "cannot open $log";
- $logging=1;
- }
-
- # load current list of processed clones
- if(open(IN,$processed_clone_list)){
- my $n=0;
- while(<IN>){
- if(/^(\S+)\s+(\S+)/){
- $processed{$1}=$2;
- $n++;
- }
- }
- close(IN);
- print "$n processed clones read from $processed_clone_list\n";
- }else{
- print "WARN: no $processed_clone_list file found\n";
- }
-
- $dbi=Bio::EnsEMBL::DBLoader->new(
- "Bio::EnsEMBL::DBSQL::DBAdaptor/host=$ihost;user=$iuser;dbname=$idbname");
-
- my $nclone=0;
- foreach my $clone_id ($dbi->get_all_Clone_id){
-
- # has clone already been processed?
- if($processed{$clone_id}){
- next;
- }
-
- $nclone++;
- last if($max_clone && $nclone>$max_clone);
-
- # is clone in one contig (finished)?
- my @contig;
- my $clone;
- eval {
- $clone=$dbi->get_Clone($clone_id);
- };
- eval{
- (@contig)=$clone->get_all_Contigs;
- };
- if($@){
- print "Contig error in Database for $clone_id:\n$@\n\n";
- next;
- }elsif(scalar(@contig)>1){
- print "$clone_id is in ".scalar(@contig)." contigs - skip\n";
- $processed{$clone_id}='unfinished';
- $nunfin++;
- next;
- }
-
- my $version=$clone->embl_version;
-
- # is clone in output database?
-# eval{
-# my $clone=$db->get_Clone($clone_id);
-# };
- #if($@){
- print "[$nclone] $clone_id not yet parsed ".
- "[$nunfin; $nnoembl; $nwrongsv; $nclonefail; ".
- "$nclonenogene; $nclonegene; $ngeneok]\n";
- my $seqio;
- eval{
- $seqio = Bio::SeqIO->new(-format => 'EMBL', -file =>
- "/usr/local/pubseq/bin/efetch emnew:$clone_id |");
- };
- if($@){
- print "$clone_id could not be fetched from EMBL - warn\n";
- $processed{$clone_id}='embl_failed';
- $nnoembl++;
- }
- &_process_file($db,$seqio,$verbose,$clone_id,$version);
- #}
-
- # else{
- # print "$clone_id already parsed - skip\n";
- # }
-
- }
-
- # write current list of checked, empty clones
- if($write){
- rename($processed_clone_list,"$processed_clone_list.old");
- if(open(OUT,">$processed_clone_list")){
- foreach my $clone_id (keys %processed){
- print OUT "$clone_id ".$processed{$clone_id}."\n";
- }
- close(OUT);
- }else{
- print "ERROR: failed writing to $processed_clone_list file\n";
- }
- close(LOG);
- }
-
-}else{
-
- # manual loading from EMBL file - for testing only
-
- if(!$clone_id && $emblfile=~/^(\w+)/){
- $clone_id=$1;
- }
-
- # delete this clone
- if($delete){
-
- # remove all genes
- foreach my $gene_id ($db->gene_Obj->get_all_Gene_id()){
- $db->gene_Obj->delete($gene_id);
- }
-
- my $clone=$db->get_Clone($clone_id);
-
- # remove clone
- $clone->delete_by_dbID;
- exit 0;
- }
-
- # link to file to be read
- my $seqio = Bio::SeqIO->new(-format => 'EMBL',-file => $emblfile);
-
- # version passed as 0 so it is not checked
- &_process_file($db,$seqio,$verbose,$clone_id,0);
-
-}
-
-# loop over entries in file
-sub _process_file{
- my($db,$seqio,$verbose,$clone_id,$version)=@_;
-
- for(;;){
-
- my $seq;
- eval{
- $seq = $seqio->next_seq;
- };
- if($@){
- print "Problem accessing EMBL file for $clone_id\n$@\n\n";
- next;
- }
- if(!$seq){
- last;
- }
-
- # check SV
- my $sv=$seq->seq_version;
- if($sv=~/^(\d+)$/){
- $sv=$1;
- if($version && $1!=$version){
- print "Sequence versions are different: Ensembl:$version; EMBL:$1\n";
- $processed{$clone_id}="embl_version:ENSEMBL:$version:EMBL:$1";
- $nwrongsv++;
- next;
- }else{
- print "Sequence versions are same: $version\n";
- }
- }else{
- print "SV could not be parsed |$sv|\n";
- next;
- }
-
- # get sequence from embl entry
- my $obj = Bio::EnsEMBL::EMBLLOAD::Obj->new(-seq => $seq);
-
- # HACK HACK HACK
- # there is only one clone to get, so don't need an id, but
- # need to set the id afterwards since it is wrong (embl_id not accession)
- my $clone = $obj->get_Clone();
- $clone->id($clone_id);
-
- # only for finished sequence, so only one contig
- my $contig;
- ($contig) = $clone->get_all_Contigs();
-
- my @genes;
- eval{
- @genes=($contig->get_all_Genes);
- };
- if($@){
- print "Problems processing clone $clone_id\n\n$@\n\n";
- if($logging){
- print LOG "$clone_id\n$@\n\n";
- }else{
- print "$@\n\n";
- }
- $nclonefail++;
- next;
- }
-
- # loop over entries to get genes and insert them into database
- my $ngene=scalar(@genes);
- if($ngene){
- $nclonegene++;
-
- # only write clone entry into database if there are genes
- if($write){
- eval{
- $db->write_Clone($clone);
- };
- if($@){
- print "Failed to write clone $clone_id\n";
- }
- }
-
- }else{
- # processing ok, but no genes
- $processed{$clone_id}='no_genes';
- $nclonenogene++;
- }
- $ngeneok+=$ngene;
- print "parsed $ngene ok [$ngeneok]\n";
-
- foreach my $gene ( @genes ) {
-
- # writeout information about gene
- if($verbose){
- my $gene_id=$gene->stable_id;
-
- foreach my $transcript ($gene->each_Transcript){
- my $transcript_id=$transcript->stable_id;
-
- }
- }
-
- # write gene to database
- if($write){
- eval{
- $db->write_Gene($gene);
-
- print STDERR "DB ID >........................................".$gene->dbID,"\t",$gene->stable_id,"\n";
-
- print GENE_MAP $gene->dbID,"\t",$gene->stable_id,"\n";
- foreach my $transcript ($gene->each_Transcript){
- print TRANSCRIPT_MAP $transcript->dbID,"\t",$transcript->stable_id,"\n";
- print TRANSLATION_MAP $transcript->translation->dbID,"\t",$transcript->translation->stable_id,"\n";
-
- foreach my $exon ($transcript->get_all_Exons){
- print EXON_MAP $exon->dbID,"\t",$exon->stable_id,"\n";
- }
-
- foreach my $dbentry ($transcript->each_DBLink){
- # attach adapter
- $dbentry->adaptor($adx);
- print STDERR "Storing ",$transcript->stable_id," ",$dbentry->primary_id,"\n";
- $adx->store($dbentry,$transcript->stable_id,'Transcript');
- }
- }
- };
- if($@){
- print "Failed to write gene ".$gene->stable_id."\n\n".$@."\n";
- }
- }
- }
- }
-}
-
-
-
-
--
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