From a156e3478815c2af101a64039d3e2468c85af82d Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 20 Jun 2003 11:01:56 +0000
Subject: [PATCH] removed old systemtests - made obsolete by healthchecks
---
systemtests/orphans_and_dangles.pl | 98 -----------
systemtests/stops_and_lengths_by_chr.pl | 205 ------------------------
systemtests/stops_and_lengths_by_fpc.pl | 200 -----------------------
3 files changed, 503 deletions(-)
delete mode 100644 systemtests/orphans_and_dangles.pl
delete mode 100755 systemtests/stops_and_lengths_by_chr.pl
delete mode 100755 systemtests/stops_and_lengths_by_fpc.pl
diff --git a/systemtests/orphans_and_dangles.pl b/systemtests/orphans_and_dangles.pl
deleted file mode 100644
index 8b880da470..0000000000
--- a/systemtests/orphans_and_dangles.pl
+++ /dev/null
@@ -1,98 +0,0 @@
-# this script check some of the foreign key relationships in ensembl style
-# database. No commandline args, you have to edit $db= line
-
-use DBI;
-use strict;
-use IO::File;
-
-my $db = DBI->connect( "dbi:mysql:host=ecs2d;database=embl_6_29_new", "ensro","" );
-
-# check if contigs are the same in embl and core
-my $count = $db->selectrow_array
- ( q{
- select count(*)
- from contig c, homo_sapiens_core_6_29.contig c2
- where c.id = c2.id
- and c.offset != c2.offset
- and c.length != c2.length
- }
- );
-
-print STDERR "$count differing contigs\n";
-
-# check if new contigs in embl not in core
-$count = $db->selectrow_array
- ( q{
- select count(*)
- from contig c
- left join homo_sapiens_core_6_29.contig c2
- on c.id = c2.id
- where c2.id is null
- }
- );
-print STDERR "new contigs in embl $count\n";
-
-
-orphan( $db, "exon", "exon_id", "exon_transcript", "exon_id" );
-orphan( $db, "exon_transcript", "exon_id", "exon", "exon_id" );
-orphan( $db, "exon", "exon_id", "exon_stable_id", "exon_id" );
-orphan( $db, "exon_stable_id", "exon_id", "exon", "exon_id" );
-
-
-orphan( $db, "transcript", "transcript_id", "exon_transcript", "transcript_id" );
-orphan( $db, "exon_transcript", "transcript_id", "transcript", "transcript_id" );
-orphan( $db, "transcript", "transcript_id", "transcript_stable_id", "transcript_id" );
-orphan( $db, "transcript_stable_id", "transcript_id", "transcript", "transcript_id" );
-
-orphan( $db, "translation", "translation_id", "transcript", "translation_id" );
-orphan( $db, "transcript", "translation_id", "translation", "translation_id" );
-
-orphan( $db, "translation", "translation_id", "translation_stable_id", "translation_id" );
-orphan( $db, "translation_stable_id", "translation_id", "translation", "translation_id" );
-
-
-orphan( $db, "gene", "gene_id", "gene_stable_id", "gene_id" );
-orphan( $db, "gene_stable_id", "gene_id", "gene", "gene_id" );
-
-orphan( $db, "gene", "gene_id", "transcript", "gene_id" );
-orphan( $db, "transcript", "gene_id", "gene", "gene_id" );
-
-orphan( $db, "objectXref", "xrefId", "Xref", "xrefId" );
-
-# very slow, now xref index on obejctXref
-# orphan( $db, "Xref", "xrefId", "objectXref", "xrefId" );
-
-
-exit;
-
-#$count = $db->selectrow_array
-# ( q{
-#
-# }
-# );
-#print STDERR "$count\n";
-
-
-sub orphan {
- my ( $db, $table1, $col1, $table2, $col2 ) = @_;
- print STDERR "Checking $table1 against $table2\n";
-
- my $count = $db->selectrow_array
- ( qq{
- select count(*)
- from $table1
- left join $table2
- on $table1.$col1 = $table2.$col2
- where $table2.$col2 is null
- }
- );
-
- if( $count > 0 ) {
- print STDERR "$count orphans on $table1, $table2\n";
- } else {
- print STDERR "Ok\n";
- }
-
-}
-
-
diff --git a/systemtests/stops_and_lengths_by_chr.pl b/systemtests/stops_and_lengths_by_chr.pl
deleted file mode 100755
index dfd6e81036..0000000000
--- a/systemtests/stops_and_lengths_by_chr.pl
+++ /dev/null
@@ -1,205 +0,0 @@
-#!/usr/local/bin/perl -w
-
-=head1 NAME
-
-Another data integrity test
-
-=head1 SYNOPSIS
-
-This script has 2 purposes:
-- check that the length of each protein is not shorter than cut-off
-given by user (default 2).
-- check that protein sequence does not contain stops ('*').
-
-How it all happens:
-- get the list of "current" chromosomes (at the present we still have
-things like chrUL_random) unless a list is given on the commandline
-- build virtual contigs for each chromosome
-- get genes on each virtual contig
-- get transcripts for each gene
-- get translation of each transcript
-- check the length of the transcript and presence of '*' characters.
-
-Output is divided to STDERR and STDOUT
-
-STDERR gets messages like:
-Now checking genes on chromosome chr1
-
-...
-
-159 genes with 172 transcripts
-
-...
-
-Checked 41 chromosomes with 335 genes with 351 transcripts
-
-Information about proteins, transcripts, genes shorter or equal to
-cut-off or containing stops id printed to STDOUT:
-
-ENSP00000211067 encoded by transcript ENST00000211067 from gene ENSG00000095908 on chromosome chrNA_random has length: 4
-
-...
-
-ENSP00000215395 encoded by transcript ENST00000215395 from gene ENSG00000099644 on chromosome chrUL_random contains '*' character(s).
-TPSQSEDLRACFEQNKFQGIATRDGLALAIGFLEPIVQNWFQNERSRQVRQHCRESRPRPGRHGPQEGR*KRTAVTGSQTALLLRAFEKDRFPGIAAREDLAR*TGLPGSRIQIRFQNRRARHLGEAGRAPAKAGSRYNAAP
-
-
-=head1 OPTIONS
-
--host db server name (default localhost)
-
--port port to connect to (default 3306)
-
--dbname name of the database to use (default ensembl_test)
-
--driver database driver (defauly mysql)
-
--user username for database access (default ensro)
-
--pass password for database access (default undef)
-
--minlength minimal length of the protein to be considered OK
-
--h|help print out help (this text)
-
-
-=head1 WARNING
-
-This script takes quite a long time to run...
-
-=head1 WARNING
-
-On big chromosomes (like chr1) one is likely to run out of memory
-(that is what happend at least on ecs1c)
-
-=cut
-
-use strict;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Getopt::Long;
-
-my $minlength = 2;
-my $host = 'localhost';
-my $port = 3306;
-my $dbname = 'ensembl100';
-my $pass = undef;
-my $user = 'ensro';
-my $driver = 'mysql';
-my $help;
-
-&GetOptions
-(
- 'host:s' => \$host,
- 'port:n' => \$port,
- 'dbname:s' => \$dbname,
- 'user:s' => \$user,
- 'pass:s' => \$pass,
- 'driver:s' => \$driver,
- 'minlength:n' => \$minlength,
- 'h|help' => \$help,
-);
-
-$help && exec('perldoc', $0);
-
-# Get db adaptor
-my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new
-(
- -user => $user,
- -dbname => $dbname,
- -host => $host,
- -driver => $driver,
- -port => $port,
- -pass => $pass,
-);
-
-
-# Get list of all current cromosomes
-my @chromosomes;
-if(@ARGV)
-{
- @chromosomes = @ARGV;
-}
-else
-{
- my $sth = $db->prepare
- (
- "select distinct(chr_name) from static_golden_path"
- );
- my $rv = $sth->execute();
- my $chr;
- $sth->bind_columns(undef, \$chr);
- while($sth->fetch)
- {
- push @chromosomes, $chr;
- }
- unless(@chromosomes) {
- die "Could not get chromosome names from static_golden_path table.\n";
- }
-}
-
-
-# Get static golden path adaptor
-my $stadp = $db->get_StaticGoldenPathAdaptor();
-
-
-# Iterate over chromosomes and pull out all genes
-my($genecount, $transcriptcount);
-foreach my $chromosome (@chromosomes)
-{
- my($chr_genecount, $chr_transcriptcount);
- print STDERR "Building virtual contig for chromosome $chromosome\n";
- my $vc = $stadp->fetch_VirtualContig_by_chr_name($chromosome);
- print STDERR "Checking genes on chromosome $chromosome\n";
- foreach my $gene ($vc->get_all_Genes)
- {
-# print $gene->id, "\n"; deleteObj($gene); next;
- $genecount++; $chr_genecount++;
- foreach my $transcript ($gene->each_Transcript)
- {
- $transcriptcount++; $chr_transcriptcount++;
- my $pep = $transcript->translate;
- my $length = length($pep->seq);
- if($length < $minlength)
- {
- print $pep->id,
- " encoded by transcript ",
- $transcript->id,
- " from gene ",
- $gene->id,
- " on chromosome ",
- $chromosome,
- " has length:\t",
- $length,
- "\n";
- }
- if($pep->seq =~ /\*/)
- {
- print $pep->id,
- " encoded by transcript ",
- $transcript->id,
- " from gene ",
- $gene->id,
- " on chromosome ",
- $chromosome,
- " contains '*' character(s).\n",
- $pep->seq,
- "\n";
- }
- } # foreach my $transcript ($gene->each_Transcript)
- deleteObj($gene);
- } # foreach my $gene (@genes)
- print STDERR "$chr_genecount genes with $chr_transcriptcount transcripts\n";
-} # foreach my $chromosome (@chromosomes)
-
-print STDERR "Checked ", scalar(@chromosomes), " chromosomes with $genecount genes with $transcriptcount transcripts\n";
-
-sub deleteObj {
- my $self = shift;
- my @dummy = values %{$self};
- foreach my $key ( keys %$self ) {
- delete $self->{$key};
- }
- foreach my $obj ( @dummy ) {
- deleteObj($obj);
- }
-}
diff --git a/systemtests/stops_and_lengths_by_fpc.pl b/systemtests/stops_and_lengths_by_fpc.pl
deleted file mode 100755
index 90908c5b1c..0000000000
--- a/systemtests/stops_and_lengths_by_fpc.pl
+++ /dev/null
@@ -1,200 +0,0 @@
-#!/usr/local/bin/perl -w
-
-=head1 NAME
-
-Another data integrity test
-
-=head1 SYNOPSIS
-
-This script has 2 purposes:
-- check that the length of each protein is not shorter than cut-off
-given by user (default 2).
-- check that protein sequence does not contain stops ('*').
-
-How it all happens:
-- get the list of fpcs
-- build virtual contigs for each fpc
-- get genes on each virtual contig
-- get transcripts for each gene
-- get translation of each transcript
-- check the length of the transcript and presence of '*' characters.
-
-Output is divided to STDERR and STDOUT
-
-STDERR gets messages like:
-Now checking genes on fpc ctg12323
-22 genes with 30 transcripts
-
-
-Information about proteins, transcripts, genes shorter than
-cut-off or containing stops id printed to STDOUT:
-
-ENSP00000228176 encoded by transcript ENST00000228176 from gene ENSG00000110736 on fpc ctg12269 contains '*' character(s).
-VKRAYLVHSAYDQSYNFIYKSFRIASII*X
-
-...
-
-ENSP00000227580 encoded by transcript ENST00000227580 from gene ENSG00000110163 on fpc ctg12475 has length: 1
-
-
-
-=head1 OPTIONS
-
--host db server name (default localhost)
-
--port port to connect to (default 3306)
-
--dbname name of the database to use (default ensembl_test)
-
--driver database driver (defauly mysql)
-
--user username for database access (default ensro)
-
--pass password for database access (default undef)
-
--minlength minimal length of the protein to be considered OK
-
--h|help print out help (this text)
-
-
-=head1 WARNING
-
-This script takes quite a long time to run...
-
-=cut
-
-use strict;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Getopt::Long;
-
-my $minlength = 2;
-my $host = 'ecs1b.sanger.ac.uk';
-my $port = 3306;
-my $dbname = 'ensembl100';
-my $pass = undef;
-my $user = 'ensro';
-my $driver = 'mysql';
-my $help;
-
-&GetOptions
-(
- 'host:s' => \$host,
- 'port:n' => \$port,
- 'dbname:s' => \$dbname,
- 'user:s' => \$user,
- 'pass:s' => \$pass,
- 'driver:s' => \$driver,
- 'minlength:n' => \$minlength,
- 'h|help' => \$help,
-);
-
-$help && exec('perldoc', $0);
-
-# Get db adaptor
-my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new
-(
- -user => $user,
- -dbname => $dbname,
- -host => $host,
- -driver => $driver,
- -port => $port,
- -pass => $pass,
-);
-
-
-# Get list of all current cromosomes
-my @fpcs;
-if(@ARGV)
-{
- @fpcs = @ARGV;
-}
-else
-{
- my $sth = $db->prepare
- (
- "select distinct(fpcctg_name) from static_golden_path"
- );
- my $rv = $sth->execute();
- my $fpc;
- $sth->bind_columns(undef, \$fpc);
- while($sth->fetch)
- {
- push @fpcs, $fpc;
- }
-}
-
-
-# Get static golden path adaptor
-my $stadp = $db->get_StaticGoldenPathAdaptor();
-
-
-# Iterate over fpcs and pull out all genes
-my($genecount, $transcriptcount, $counter) = (0, 0, 0);
-foreach my $fpc (@fpcs)
-{
- my($fpc_genecount, $fpc_transcriptcount) = (0, 0);
- print STDERR "Building virtual contig for fpc $fpc\n";
- my $vc = $stadp->fetch_VirtualContig_by_fpc_name($fpc);
- print STDERR "Now checking genes on fpc $fpc\n";
- foreach my $gene ($vc->get_all_Genes)
- {
- $genecount++; $fpc_genecount++;
- foreach my $transcript ($gene->each_Transcript)
- {
- $transcriptcount++; $fpc_transcriptcount++;
- my $pep = $transcript->translate;
- my $length = length($pep->seq);
- if($length < $minlength)
- {
- print $pep->id,
- " encoded by transcript ",
- $transcript->id,
- " from gene ",
- $gene->id,
- " on fpc ",
- $fpc,
- " has length:\t",
- $length,
- "\n";
- }
- if($pep->seq =~ /\*/)
- {
- print $pep->id,
- " encoded by transcript ",
- $transcript->id,
- " from gene ",
- $gene->id,
- " on fpc ",
- $fpc,
- " contains '*' character(s).\n",
- $pep->seq,
- "\n";
- }
- deleteObj($pep);
- deleteObj($transcript);
- } # foreach my $transcript ($gene->each_Transcript)
- deleteObj($gene);
- } # foreach my $gene (@genes)
- print STDERR "$fpc_genecount genes with $fpc_transcriptcount transcripts\n";
- deleteObj($fpc);
-} # foreach my $fpc (@fpcs)
-
-print STDERR "Checked ", scalar(@fpcs), " fpcs with $genecount genes with $transcriptcount transcripts\n";
-
-
-sub deleteObj {
- my $self = shift;
- eval{
- my @dummy = values %{$self};
- foreach my $key ( keys %$self ) {
- delete $self->{$key};
- }
- foreach my $obj ( @dummy ) {
- deleteObj($obj);
- }
- };
-}
-
-
-
-
--
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