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ensembl-gh-mirror
ensembl
Commits
aba8ca2c
Commit
aba8ca2c
authored
May 17, 2005
by
Patrick Meidl
Browse files
changes from branch-vega-30-dev
parent
cbfefbe1
Changes
15
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Showing
15 changed files
with
408 additions
and
363 deletions
+408
-363
misc-scripts/density_feature/glovar_snp_density.pl
misc-scripts/density_feature/glovar_snp_density.pl
+3
-3
misc-scripts/density_feature/glovar_snp_wrapper.pl
misc-scripts/density_feature/glovar_snp_wrapper.pl
+3
-3
misc-scripts/density_feature/vega_gene_density.pl
misc-scripts/density_feature/vega_gene_density.pl
+5
-3
misc-scripts/density_feature/vega_percent_gc_calc.pl
misc-scripts/density_feature/vega_percent_gc_calc.pl
+2
-2
misc-scripts/density_feature/vega_repeat_coverage_calc.pl
misc-scripts/density_feature/vega_repeat_coverage_calc.pl
+2
-2
misc-scripts/surgery/SeqStoreConverter/BasicConverter.pm
misc-scripts/surgery/SeqStoreConverter/BasicConverter.pm
+5
-5
misc-scripts/surgery/SeqStoreConverter/vega/CanisFamiliaris.pm
...scripts/surgery/SeqStoreConverter/vega/CanisFamiliaris.pm
+1
-1
misc-scripts/surgery/SeqStoreConverter/vega/DanioRerio.pm
misc-scripts/surgery/SeqStoreConverter/vega/DanioRerio.pm
+120
-62
misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm
misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm
+1
-1
misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm
misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm
+1
-1
misc-scripts/surgery/SeqStoreConverter/vega/VBasicConverter.pm
...scripts/surgery/SeqStoreConverter/vega/VBasicConverter.pm
+84
-67
misc-scripts/surgery/converter.input
misc-scripts/surgery/converter.input
+2
-2
modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+60
-12
modules/Bio/EnsEMBL/Utils/SchemaConversion.pm
modules/Bio/EnsEMBL/Utils/SchemaConversion.pm
+94
-96
sql/vega_specific_tables.sql
sql/vega_specific_tables.sql
+25
-103
No files found.
misc-scripts/density_feature/glovar_snp_density.pl
View file @
aba8ca2c
...
...
@@ -11,7 +11,7 @@ index dumps) for Vega.
./glovar_snp_density.pl
--species=Homo_sapiens
[--chr=6,13,14]
[--dry
-
run|-n]
[--dry
_
run|-n]
[--avdump|-a]
[--help|-h]
...
...
@@ -65,7 +65,7 @@ my ($species, $chr, $dry, $avdump, $help);
&GetOptions
(
"
species=s
"
=>
\
$species
,
"
chr=s
"
=>
\
$chr
,
"
dry
-
run
"
=>
\
$dry
,
"
dry
_
run
"
=>
\
$dry
,
"
n
"
=>
\
$dry
,
"
avdump
"
=>
\
$avdump
,
"
a
"
=>
\
$avdump
,
...
...
@@ -78,7 +78,7 @@ if($help || !$species){
./glovar_snp_density.pl
--species=Homo_sapiens
[--chr=6,13,14]
[--dry
-
run|-n]
[--dry
_
run|-n]
[--avdump|-a]
[--help|-h]\n\n)
;
exit
;
...
...
misc-scripts/density_feature/glovar_snp_wrapper.pl
View file @
aba8ca2c
...
...
@@ -9,7 +9,7 @@ Wrapper for glovar_snp_density.pl
./glovar_snp_density.pl
--species=Homo_sapiens
[--dry
-
run|-n]
[--dry
_
run|-n]
[--avdump|-a]
=head1 DESCRIPTION
...
...
@@ -53,7 +53,7 @@ use Getopt::Long;
my
(
$species
,
$dry
,
$avdump
);
&GetOptions
(
"
species=s
"
=>
\
$species
,
"
dry
-
run
"
=>
\
$dry
,
"
dry
_
run
"
=>
\
$dry
,
"
n
"
=>
\
$dry
,
"
avdump
"
=>
\
$avdump
,
"
a
"
=>
\
$avdump
,
...
...
@@ -64,7 +64,7 @@ unless ($species) {
./glovar_snp_density.pl
--species=Homo_sapiens
[--avdump|-a]
[--dry
-
run|-n]\n\n)
;
[--dry
_
run|-n]\n\n)
;
exit
;
}
...
...
misc-scripts/density_feature/vega_gene_density.pl
View file @
aba8ca2c
...
...
@@ -9,7 +9,7 @@ script to calculate gene densities and stats in Vega
./vega_gene_density.pl
--species=Homo_sapiens
[--dry
-
run|-n]
[--dry
_
run|-n]
[--help|-h]
=head1 DESCRIPTION
...
...
@@ -63,7 +63,7 @@ my ($species, $chr, $dry, $help);
&GetOptions
(
"
species=s
"
=>
\
$species
,
"
chr=s
"
=>
\
$chr
,
"
dry
-
run
"
=>
\
$dry
,
"
dry
_
run
"
=>
\
$dry
,
"
n
"
=>
\
$dry
,
"
help
"
=>
\
$help
,
"
h
"
=>
\
$help
,
...
...
@@ -74,7 +74,7 @@ if($help || !$species){
./vega_gene_density.pl
--species=Homo_sapiens
[--chr=1,2]
[--dry
-
run|-n]
[--dry
_
run|-n]
[--help|-h]\n\n)
;
exit
;
}
...
...
@@ -125,6 +125,8 @@ for my $slice ( @top_slices ) {
}
$big_block_size
=
int
(
$min_big_chr
/
150
);
#use this size if another human is needed
#$big_block_size = 28050;
push
@
{
$big_chr
},
$big_block_size
;
$small_block_size
=
int
(
$min_small_chr
/
150
);
push
@
{
$small_chr
},
$small_block_size
;
...
...
misc-scripts/density_feature/vega_percent_gc_calc.pl
View file @
aba8ca2c
...
...
@@ -31,7 +31,7 @@ use Data::Dumper;
my
(
$species
,
$dry
,
$help
);
&GetOptions
(
"
species=s
"
=>
\
$species
,
"
dry
-
run
"
=>
\
$dry
,
"
dry
_
run
"
=>
\
$dry
,
"
n
"
=>
\
$dry
,
"
help
"
=>
\
$help
,
"
h
"
=>
\
$help
,
...
...
@@ -41,7 +41,7 @@ if($help || !$species){
print
qq(Usage:
./vega_gene_density.pl
--species=Homo_sapiens
[--dry
-
run|-n]
[--dry
_
run|-n]
[--help|-h]\n\n)
;
exit
;
}
...
...
misc-scripts/density_feature/vega_repeat_coverage_calc.pl
View file @
aba8ca2c
...
...
@@ -32,7 +32,7 @@ use Data::Dumper;
my
(
$species
,
$dry
,
$help
);
&GetOptions
(
"
species=s
"
=>
\
$species
,
"
dry
-
run
"
=>
\
$dry
,
"
dry
_
run
"
=>
\
$dry
,
"
n
"
=>
\
$dry
,
"
help
"
=>
\
$help
,
"
h
"
=>
\
$help
,
...
...
@@ -42,7 +42,7 @@ if($help || !$species){
print
qq(Usage:
./vega_gene_density.pl
--species=Homo_sapiens
[--dry
-
run|-n]
[--dry
_
run|-n]
[--help|-h]\n\n)
;
exit
;
}
...
...
misc-scripts/surgery/SeqStoreConverter/BasicConverter.pm
View file @
aba8ca2c
...
...
@@ -56,13 +56,13 @@ sub new {
$self
->
debug
("
Building schema for
$target
from
$schema
");
die
"
Cannot open
$schema
"
if
(
!
-
e
$schema
);
my
$cmd
=
"
mysql -u
$user
-p
$pass
-P
$port
-h
$host
$target
<
$schema
";
my
$cmd
=
"
/usr/local/mysql/bin/
mysql -u
$user
-p
$pass
-P
$port
-h
$host
$target
<
$schema
";
system
(
$cmd
);
if
(
$vega_schema
)
{
$self
->
debug
("
Adding vega tables for
$target
");
die
"
Cannot open vega creation script
"
if
(
!
-
e
$vega_schema
);
my
$cmd
=
"
mysql -u
$user
-p
$pass
-P
$port
-h
$host
$target
<
$vega_schema
";
my
$cmd
=
"
/usr/local/mysql/bin/
mysql -u
$user
-p
$pass
-P
$port
-h
$host
$target
<
$vega_schema
";
system
(
$cmd
);
}
...
...
@@ -851,7 +851,7 @@ sub transfer_features {
"
contig_strand, analysis_id, repeat_start, repeat_end,
"
.
"
repeat_consensus_id, score FROM
$source
.repeat_feature
$limit
");
$self
->
debug
("
Read
d
ing indexes on repeat_feature
");
$self
->
debug
("
Reading indexes on repeat_feature
");
$dbh
->
do
("
ALTER TABLE
$target
.repeat_feature
"
.
"
ADD INDEX seq_region_idx( seq_region_id, seq_region_start)
");
$dbh
->
do
("
ALTER TABLE
$target
.repeat_feature
"
.
...
...
@@ -875,7 +875,7 @@ sub transfer_features {
"
hit_end, hit_name, cigar_line, evalue, perc_ident, score
"
.
"
FROM
$source
.protein_align_feature
$limit
");
$self
->
debug
("
Read
d
ing indexes on protein_align_feature
");
$self
->
debug
("
Reading indexes on protein_align_feature
");
$dbh
->
do
(
qq{ALTER TABLE $target.protein_align_feature
ADD index seq_region_idx( analysis_id, seq_region_id,
seq_region_start, score )}
);
...
...
@@ -899,7 +899,7 @@ sub transfer_features {
"
perc_ident, score FROM
$source
.dna_align_feature
$limit
");
$self
->
debug
("
Read
d
ing indexes on dna_align_feature
");
$self
->
debug
("
Reading indexes on dna_align_feature
");
$dbh
->
do
(
qq{ALTER TABLE $target.dna_align_feature
ADD INDEX seq_region_idx(seq_region_id, analysis_id,
seq_region_start, score)}
);
...
...
misc-scripts/surgery/SeqStoreConverter/vega/CanisFamiliaris.pm
View file @
aba8ca2c
...
...
@@ -8,7 +8,7 @@ use SeqStoreConverter::vega::VBasicConverter;
use
vars
qw(@ISA)
;
@ISA
=
qw(SeqStoreConverter::
vega::VBasicConverter SeqStoreConverter::CanisFamiliaris
)
;
@ISA
=
qw(SeqStoreConverter::
CanisFamiliaris SeqStoreConverter::vega::VBasicConverter
)
;
1
;
misc-scripts/surgery/SeqStoreConverter/vega/DanioRerio.pm
View file @
aba8ca2c
...
...
@@ -7,7 +7,7 @@ use SeqStoreConverter::DanioRerio;
use
SeqStoreConverter::vega::
VBasicConverter
;
use
vars
qw(@ISA)
;
@ISA
=
qw(SeqStoreConverter::vega::VBasicConverter
SeqStoreConverter::DanioRerio
)
;
@ISA
=
qw(
SeqStoreConverter::DanioRerio
SeqStoreConverter::vega::VBasicConverter)
;
sub
copy_internal_clone_names
{
my
$self
=
shift
;
...
...
@@ -20,7 +20,7 @@ sub copy_internal_clone_names {
#get id for 'fpc_clone_id' attribute
$dbh
->
do
("
INSERT INTO
$target
.attrib_type (code,name,description)
"
.
"
values ('fpc_clone_id','fpc clone','clone id used for linking to Zebrafish webFPC')
");
"
values ('fpc_clone_id','fpc clone','clone id used for linking to Zebrafish webFPC')
");
my
(
$attrib_id
)
=
$dbh
->
selectrow_array
("
Select attrib_type_id from
$target
.attrib_type where code = 'fpc_clone_id'
");
warn
"
No attrib id found
\n
"
unless
defined
(
$attrib_id
);
...
...
@@ -38,69 +38,127 @@ sub copy_internal_clone_names {
my
$insert_sth
=
$dbh
->
prepare
("
insert into
$target
.seq_region_attrib values (?,
$attrib_id
,?)
");
while
(
$select1_sth
->
fetch
())
{
$embl_name
=~
s/([\d\w]+).*/$1/
;
$select2_sth
->
bind_param
(
1
,
$embl_name
);
$select2_sth
->
execute
;
$insert_sth
->
bind_param
(
1
,
$seq_region_id
);
while
(
my
(
$clone_name
)
=
$select2_sth
->
fetchrow_array
())
{
$insert_sth
->
bind_param
(
2
,
$clone_name
);
$insert_sth
->
execute
();
}
}
$embl_name
=~
s/([\d\w]+).*/$1/
;
$select2_sth
->
bind_param
(
1
,
$embl_name
);
$select2_sth
->
execute
;
$insert_sth
->
bind_param
(
1
,
$seq_region_id
);
while
(
my
(
$clone_name
)
=
$select2_sth
->
fetchrow_array
())
{
$insert_sth
->
bind_param
(
2
,
$clone_name
);
$insert_sth
->
execute
();
}
}
}
sub
update_clone_info
{
my
$self
=
shift
;
my
$target_cs_name
=
shift
;
my
$target
=
$self
->
target
();
my
$source
=
$self
->
source
();
my
$dbh
=
$self
->
dbh
();
$self
->
debug
("
Vega Danio_specific - Transforming clone_id into seq_region_id for clone_info and current_clone_info
");
foreach
my
$table_name
('
clone_info
','
current_clone_info
')
{
my
$select_st1
=
"
SELECT ctg.name, ctg.clone_id
"
.
"
FROM
$source
.contig ctg,
$source
.
$table_name
ci
"
.
"
WHERE ctg.clone_id = ci.clone_id
"
.
"
AND ctg.name not like 'ctg%'
"
.
"
AND ctg.name not like 'NA%'
";
my
$query_results1
=
$dbh
->
selectall_arrayref
(
$select_st1
);
my
$i
=
0
;
foreach
my
$contig_name
(
@$query_results1
)
{
my
$embl_acc
=
$contig_name
->
[
0
];
my
$select_st2
=
"
SELECT sr.seq_region_id
"
.
"
FROM
$target
.seq_region sr
"
.
"
WHERE sr.name = '
$embl_acc
'
";
my
@query_results2
=
$dbh
->
selectrow_array
(
$select_st2
);
push
@
{
$query_results1
->
[
$i
]},
@query_results2
;
$i
++
;
}
foreach
my
$clone
(
@$query_results1
)
{
my
$seq_reg_id
=
$clone
->
[
2
];
my
$clone_id
=
$clone
->
[
1
];
my
$update_query
=
"
UPDATE
$target
.
$table_name
"
.
"
SET clone_id = '
$seq_reg_id
'
"
.
"
WHERE clone_id = '
$clone_id
'
";
$dbh
->
do
(
$update_query
);
}
my
$alter_struct_1
=
"
ALTER table
$target
.
$table_name
"
.
"
CHANGE clone_id seq_region_id int(10) not null
";
my
$alter_struct_2
=
"
ALTER table
$target
.
$table_name
"
.
"
add unique index (seq_region_id)
";
$dbh
->
do
(
$alter_struct_1
);
$dbh
->
do
(
$alter_struct_2
);
}
}
my
$self
=
shift
;
my
$target_cs_name
=
shift
;
my
$target
=
$self
->
target
();
my
$source
=
$self
->
source
();
my
$dbh
=
$self
->
dbh
();
# clone_info, current_clone_info
$self
->
debug
("
Vega Danio_specific - Transforming clone_id into seq_region_id for clone_info and current_clone_info
");
foreach
my
$table_name
('
clone_info
','
current_clone_info
')
{
my
$select_st1
=
"
SELECT ctg.name, ctg.clone_id
"
.
"
FROM
$source
.contig ctg,
$source
.
$table_name
ci
"
.
"
WHERE ctg.clone_id = ci.clone_id
"
.
"
AND ctg.name not like 'ctg%'
"
.
"
AND ctg.name not like 'NA%'
";
my
$query_results1
=
$dbh
->
selectall_arrayref
(
$select_st1
);
my
$i
=
0
;
foreach
my
$contig_name
(
@$query_results1
)
{
my
$embl_acc
=
$contig_name
->
[
0
];
my
$select_st2
=
"
SELECT sr.seq_region_id
"
.
"
FROM
$target
.seq_region sr
"
.
"
WHERE sr.name = '
$embl_acc
'
";
my
@query_results2
=
$dbh
->
selectrow_array
(
$select_st2
);
push
@
{
$query_results1
->
[
$i
]},
@query_results2
;
$i
++
;
}
foreach
my
$clone
(
@$query_results1
)
{
my
$seq_reg_id
=
$clone
->
[
2
];
my
$clone_id
=
$clone
->
[
1
];
my
$update_query
=
"
UPDATE
$target
.
$table_name
"
.
"
SET clone_id = '
$seq_reg_id
'
"
.
"
WHERE clone_id = '
$clone_id
'
";
$dbh
->
do
(
$update_query
);
}
my
$alter_struct_1
=
"
ALTER table
$target
.
$table_name
"
.
"
CHANGE clone_id seq_region_id int(10) not null
";
my
$alter_struct_2
=
"
ALTER table
$target
.
$table_name
"
.
"
add unique index (seq_region_id)
";
$dbh
->
do
(
$alter_struct_1
);
$dbh
->
do
(
$alter_struct_2
);
}
# assembly_tag
$self
->
debug
("
Vega Danio_specific - Transforming contig_id into seq_region_id for assembly_tag
");
# first remove orphans from assembly_tag table (i.e. entries pointing to
# non-existing contigs)
my
$numrows
=
$dbh
->
do
(
qq(
DELETE at
FROM $source.assembly_tag at
LEFT JOIN $source.contig c ON c.contig_id = at.contig_id
WHERE c.contig_id IS NULL
)
);
$self
->
debug
("
Deleted
$numrows
orphans from assembly_tag
");
my
$select_st3
=
"
SELECT ctg.name, ctg.contig_id
"
.
"
FROM
$source
.contig ctg,
$source
.assembly_tag at
"
.
"
WHERE ctg.contig_id = at.contig_id
"
.
"
AND ctg.name not like 'ctg%'
"
.
"
AND ctg.name not like 'NA%'
";
my
$query_results3
=
$dbh
->
selectall_arrayref
(
$select_st3
);
my
$j
=
0
;
foreach
my
$contig_name
(
@$query_results3
)
{
my
$embl_acc
=
$contig_name
->
[
0
];
my
$select_st4
=
"
SELECT sr.seq_region_id
"
.
"
FROM
$target
.seq_region sr
"
.
"
WHERE sr.name = '
$embl_acc
'
";
my
@query_results4
=
$dbh
->
selectrow_array
(
$select_st4
);
push
@
{
$query_results3
->
[
$j
]},
@query_results4
;
$j
++
;
}
foreach
my
$contig
(
@$query_results3
)
{
my
$seq_reg_id
=
$contig
->
[
2
];
my
$contig_id
=
$contig
->
[
1
];
my
$update_query
=
"
UPDATE
$target
.assembly_tag
"
.
"
SET contig_id = '
$seq_reg_id
'
"
.
"
WHERE contig_id = '
$contig_id
'
";
$dbh
->
do
(
$update_query
);
}
$dbh
->
do
("
ALTER TABLE
$target
.assembly_tag
CHANGE contig_id seq_region_id int(10) UNSIGNED NOT NULL
");
$dbh
->
do
("
ALTER TABLE
$target
.assembly_tag
CHANGE contig_start seq_region_start int(10)
");
$dbh
->
do
("
ALTER TABLE
$target
.assembly_tag
CHANGE contig_end seq_region_end int(10)
");
$dbh
->
do
("
ALTER TABLE
$target
.assembly_tag
CHANGE contig_strand seq_region_strand tinyint(1)
");
}
1
;
misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm
View file @
aba8ca2c
...
...
@@ -8,6 +8,6 @@ use SeqStoreConverter::vega::VBasicConverter;
use
vars
qw(@ISA)
;
@ISA
=
qw(SeqStoreConverter::
vega::VBasicConverter SeqStoreConverter::HomoSapiens
)
;
@ISA
=
qw(SeqStoreConverter::
HomoSapiens SeqStoreConverter::vega::VBasicConverter
)
;
1
;
misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm
View file @
aba8ca2c
...
...
@@ -8,6 +8,6 @@ use SeqStoreConverter::vega::VBasicConverter;
use
vars
qw(@ISA)
;
@ISA
=
qw(SeqStoreConverter::
vega::VBasicConverter SeqStoreConverter::MusMusculus
)
;
@ISA
=
qw(SeqStoreConverter::
MusMusculus SeqStoreConverter::vega::VBasicConverter
)
;
1
;
misc-scripts/surgery/SeqStoreConverter/vega/VBasicConverter.pm
View file @
aba8ca2c
package
SeqStoreConverter::vega::
VBasicConverter
;
use
strict
;
use
warnings
;
use
SeqStoreConverter::
BasicConverter
;
package
SeqStoreConverter::vega::
VBasicConverter
;
use
vars
qw(@ISA)
;
@ISA
=
qw(SeqStoreConverter::BasicConverter)
;
sub
remove_supercontigs
{
my
$self
=
shift
;
...
...
@@ -18,62 +14,41 @@ sub remove_supercontigs {
$self
->
debug
("
Vega specific - removing supercontigs from
$target
");
$dbh
->
do
("
DELETE FROM
$target
.meta
"
.
"
WHERE meta_value like '%supercontig%'
");
"
WHERE meta_value like '%supercontig%'
");
$dbh
->
do
("
DELETE FROM
$target
.coord_system
"
.
"
WHERE name like 'supercontig'
");
"
WHERE name like 'supercontig'
");
$dbh
->
do
("
DELETE
$target
.a
"
.
"
FROM
$target
.assembly a,
$target
.seq_region sr
"
.
"
WHERE sr.coord_system_id = 2
"
.
"
and a.asm_seq_region_id = sr.seq_region_id
");
"
FROM
$target
.assembly a,
$target
.seq_region sr
"
.
"
WHERE sr.coord_system_id = 2
"
.
"
and a.asm_seq_region_id = sr.seq_region_id
");
$dbh
->
do
("
DELETE FROM
$target
.seq_region
"
.
"
WHERE coord_system_id = 2
");
"
WHERE coord_system_id = 2
");
}
sub
copy_other_tables
{
my
$self
=
shift
;
#xref tables
$self
->
copy_tables
("
xref
",
"
go_xref
",
"
identity_xref
",
"
object_xref
",
"
external_db
",
"
external_synonym
",
#marker/qtl related tables
"
map
",
"
marker
",
"
marker_synonym
",
"
qtl
",
"
qtl_synonym
",
#misc other tables
"
supporting_feature
",
"
analysis
",
"
exon_transcript
",
"
interpro
",
"
gene_description
",
"
protein_feature
",
#vega tables
"
gene_synonym
",
"
transcript_info
",
"
current_gene_info
",
"
current_transcript_info
",
"
author
",
"
gene_name
",
"
transcript_class
",
"
gene_remark
",
"
gene_info
",
"
evidence
",
"
transcript_remark
",
"
clone_remark
",
"
clone_info
",
"
clone_info_keyword
",
"
clone_lock
");
$self
->
copy_current_clone_info
;
sub
copy_other_vega_tables
{
my
$self
=
shift
;
$self
->
copy_tables
(
# vega tables
"
gene_synonym
",
"
transcript_info
",
"
current_gene_info
",
"
current_transcript_info
",
"
author
",
"
gene_name
",
"
transcript_class
",
"
gene_remark
",
"
gene_info
",
"
evidence
",
"
transcript_remark
",
"
clone_remark
",
"
clone_info
",
"
clone_info_keyword
",
"
assembly_tag
",
);
$self
->
copy_current_clone_info
;
}
sub
copy_current_clone_info
{
...
...
@@ -86,22 +61,64 @@ sub copy_current_clone_info {
$sth
->
finish
();
}
sub
update_genscan
{
my
$self
=
shift
;
$self
->
debug
("
Vega specific - updating analysis name for Genscans
");
my
$target
=
$self
->
target
();
my
$sth
=
$self
->
dbh
()
->
prepare
("
UPDATE
$target
.analysis set logic_name = 'Vega_Genscan' where logic_name = 'Genscan'
");
$sth
->
execute
();
$sth
->
finish
();
}
sub
update_clone_info
{
my
$self
=
shift
;
return
;
my
$self
=
shift
;
return
;
}
sub
copy_internal_clone_names
{
my
$self
=
shift
;
my
$self
=
shift
;
return
;
}
sub
copy_assembly_exception
{
my
$self
=
shift
;
# copy assembly_exception table
$self
->
debug
('
Vega specific - copying assembly_exception table
');
$self
->
copy_tables
('
assembly_exception
');
my
$source
=
$self
->
source
();
my
$target
=
$self
->
target
();
my
$dbh
=
$self
->
dbh
();
# fix seq_region_id in assembly_exception
$self
->
debug
('
Vega specific - Updating seq_region_id in assembly_exception table
');
$dbh
->
do
(
qq(
UPDATE $target.assembly_exception, $target.tmp_chr_map
SET assembly_exception.seq_region_id = tmp_chr_map.new_id
WHERE assembly_exception.seq_region_id = tmp_chr_map.old_id
)
);
$dbh
->
do
(
qq(
UPDATE $target.assembly_exception, $target.tmp_chr_map
SET assembly_exception.exc_seq_region_id = tmp_chr_map.new_id
WHERE assembly_exception.exc_seq_region_id = tmp_chr_map.old_id
)
);
# fix seq_region.length if necessary (this is the case if you have an
# assembly_exception at the end of a chromosome)
my
$sth1
=
$dbh
->
prepare
(
qq(
UPDATE $target.seq_region SET length = ? WHERE seq_region_id = ?
)
);
my
$sth2
=
$dbh
->
prepare
(
qq(
SELECT
sr.seq_region_id,
sr.length,
max(ae.seq_region_end)
FROM
$target.seq_region sr,
$target.assembly_exception ae
WHERE sr.seq_region_id = ae.seq_region_id
GROUP BY ae.seq_region_id
)
);
$sth2
->
execute
;
while
(
my
(
$sr_id
,
$sr_length
,
$max_ae_length
)
=
$sth2
->
fetchrow_array
)
{
if
(
$max_ae_length
>
$sr_length
)
{
$self
->
debug
("
Updating seq_region.length for
$sr_id
(old
$sr_length
, new
$max_ae_length
)
");
$sth1
->
execute
(
$max_ae_length
,
$sr_id
);
}
}
}
misc-scripts/surgery/converter.input
View file @
aba8ca2c
#
HomoSapiens ecs
1d mcvicker_old_schema mcvicker_new_schema
HomoSapiens ecs
3:3307 mouse_vega040719_raw pm2_mouse_vega040719
#FuguRubripes ecs2f fugu_rubripes_core_18_2 mcvicker_new_fugu
CaenorhabditisElegans ecs2f caenorhabditis_elegans_core_18_102 mcvicker_new_elegans
#
CaenorhabditisElegans ecs2f caenorhabditis_elegans_core_18_102 mcvicker_new_elegans
#CaenorhabditisBriggsae ecs2f caenorhabditis_briggsae_core_18_25 mcvicker_new_briggsae
#RattusNorvegicus ecs2f rattus_norvegicus_core_18_3 mcvicker_new_rat
#DrosophilaMelanogaster ecs2f drosophila_melanogaster_core_18_3a mcvicker_new_fly
...
...