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ensembl-gh-mirror
ensembl
Commits
4312cdc1
Commit
4312cdc1
authored
Nov 12, 2010
by
Ian Longden
Browse files
Allow multiple assembly exceptions and store synonyms of slice (seq region synonym) if they exist
parent
ed44972d
Changes
1
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1 changed file
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63 additions
and
19 deletions
+63
-19
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+63
-19
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modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
View file @
4312cdc1
...
...
@@ -290,6 +290,20 @@ sub fetch_by_region {
if
(
$sth
->
rows
()
==
0
)
{
$sth
->
finish
();
# try synonyms
my
$syn_sql_sth
=
$self
->
prepare
("
select s.name from seq_region s, seq_region_synonym ss where s.seq_region_id = ss.seq_region_id and ss.synonym = ?
");
$syn_sql_sth
->
bind_param
(
1
,
$seq_region_name
,
SQL_VARCHAR
);
$syn_sql_sth
->
execute
();
my
$new_name
;
$syn_sql_sth
->
bind_columns
(
\
$new_name
);
if
(
$syn_sql_sth
->
fetch
){
$syn_sql_sth
->
finish
;
return
$self
->
fetch_by_region
(
$coord_system_name
,
$new_name
,
$start
,
$end
,
$strand
,
$version
,
$no_fuzz
);
}
$syn_sql_sth
->
finish
;
if
(
$no_fuzz
)
{
return
undef
}
# Do fuzzy matching, assuming that we are just missing a version
...
...
@@ -1374,40 +1388,62 @@ sub fetch_normalized_slice_projection {
}
my
@syms
;
if
(
@haps
>
1
)
{
if
(
@haps
>
=
1
)
{
my
@sort_haps
=
sort
{
$a
->
[
1
]
<=>
$b
->
[
1
]
}
@haps
;
throw
(
"
More than one HAP region not supported yet
"
);
}
elsif
(
@haps
==
1
)
{
my
$hap
=
$haps
[
0
];
my
$seq_reg_slice
=
$self
->
fetch_by_seq_region_id
(
$slice_seq_region_id
);
my
$exc_slice
=
$self
->
fetch_by_seq_region_id
(
$hap
->
[
2
]
);
my
$count
=
0
;
my
$chr_start
=
1
;
my
$hap_start
=
1
;
my
$last
=
0
;
#
# lengths of haplotype and reference in db may be different
# we want to use the maximum possible length for the mapping
# between the two systems
#
my
$seq_reg_slice
=
$self
->
fetch_by_seq_region_id
(
$slice_seq_region_id
);
my
$exc_slice
=
$self
->
fetch_by_seq_region_id
(
$sort_haps
[
0
][
2
]
);
my
$len1
=
$seq_reg_slice
->
length
();
my
$len2
=
$exc_slice
->
length
();
my
$max_len
=
(
$len1
>
$len2
)
?
$len1
:
$len2
;
#the inserted region can differ in length, but mapped sections
#need to be same lengths
my
$diff
=
$hap
->
[
4
]
-
$hap
->
[
1
];
while
(
$count
<=
scalar
(
@sort_haps
)
and
!
$last
){
my
$chr_end
;
my
$hap_end
;
if
(
defined
(
$sort_haps
[
$count
])
and
defined
(
$sort_haps
[
$count
][
0
])
){
$hap_end
=
$sort_haps
[
$count
][
0
]
-
1
;
$chr_end
=
$sort_haps
[
$count
][
3
]
-
1
}
else
{
$last
=
1
;
$hap_end
=
$len1
;
$chr_end
=
$len2
;
my
$diff
=
(
$hap_end
-
$hap_start
)
-
(
$chr_end
-
$chr_start
);
if
(
$diff
>
0
){
push
(
@syms
,
[
$hap_start
,
$hap_end
,
$sort_haps
[
0
][
2
],
$chr_start
,
$chr_end
+
$diff
]
);
}
elsif
(
$diff
<
0
){
push
(
@syms
,
[
$hap_start
,
$hap_end
+
$diff
,
$sort_haps
[
0
][
2
],
$chr_start
,
$chr_end
]
);
}
else
{
push
(
@syms
,
[
$hap_start
,
$hap_end
,
$sort_haps
[
0
][
2
],
$chr_start
,
$chr_end
]
);
}
next
;
}
if
(
$hap_end
and
$hap_start
<
$len1
){
# if hap at start or end of chromosome
push
(
@syms
,
[
$hap_start
,
$hap_end
,
$sort_haps
[
0
][
2
],
$chr_start
,
$chr_end
]
);
}
$chr_start
=
$chr_end
+
(
$sort_haps
[
$count
][
4
]
-
$sort_haps
[
$count
][
3
])
+
2
;
$hap_start
=
$hap_end
+
(
$sort_haps
[
$count
][
1
]
-
$sort_haps
[
$count
][
0
])
+
2
;
$count
++
;
}
# we want the region of the haplotype INVERTED
push
(
@syms
,
[
1
,
$hap
->
[
0
]
-
1
,
$hap
->
[
2
],
1
,
$hap
->
[
3
]
-
1
]
);
push
(
@syms
,
[
$hap
->
[
1
]
+
1
,
$max_len
-
$diff
,
$hap
->
[
2
],
$hap
->
[
4
]
+
1
,
$max_len
]
);
}
# for now haps and pars should not be both there, but in theory we
# could handle it here by cleverly merging the pars into the existing syms,
# for now just:
push
(
@syms
,
@pars
);
my
$mapper
=
Bio::EnsEMBL::
Mapper
->
new
(
"
sym
",
"
org
"
);
my
$count
=
0
;
for
my
$sym
(
@syms
)
{
$mapper
->
add_map_coordinates
(
$slice_seq_region_id
,
$sym
->
[
0
],
$sym
->
[
1
],
1
,
$sym
->
[
2
],
$sym
->
[
3
],
$sym
->
[
4
]
);
...
...
@@ -1581,6 +1617,15 @@ sub store {
$seq_adaptor
->
store
(
$seq_region_id
,
$$seqref
);
}
#synonyms
if
(
defined
(
$slice
->
{'
synonym
'})){
foreach
my
$syn
(
@
{
$slice
->
{'
synonym
'}}
){
$syn
->
seq_region_id
(
$seq_region_id
);
# set the seq_region_id
$syn
->
adaptor
->
store
(
$syn
);
}
}
$slice
->
adaptor
(
$self
);
return
$seq_region_id
;
...
...
@@ -1819,7 +1864,6 @@ LSQL
}
## end sub cache_toplevel_seq_mappings
#####################################
# sub DEPRECATED METHODs
#####################################
...
...
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