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F73302351
getVariants.php
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Created
Sat, Jul 20, 10:30
Size
2 KB
Mime Type
text/x-php
Expires
Mon, Jul 22, 10:30 (2 d)
Engine
blob
Format
Raw Data
Handle
19179688
Attached To
R2664 SHRINE MedCo Fork
getVariants.php
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<?php
// query_type define is we are searching by:
// - old is the old version that uses the first version of the schema
// - Gene + Zygosity
// - ...
$query
=
""
;
switch
(
$_GET
[
"query_type"
]){
case
"gene_and_zygosity"
:
// case insensitive regex query
// select variant_id
// from shrine_ont.genomic_annotations_new
// where annotations ~* '^CTBP2P1;(Homozygous|Unknown);'
$zigosity
=
$_GET
[
"zygosity"
];
// array of zygosity options, put them in the query separated by | (or)
$query
=
"SELECT variant_id "
.
"FROM shrine_ont.genomic_annotations_new "
.
"WHERE annotations ~* '^"
.
$_GET
[
"gene_name"
]
.
";("
.
join
(
'|'
,
$zigosity
)
.
");'"
;
break
;
case
"variantName_and_zygosity"
:
// select variant_id
// from shrine_ont.genomic_annotations_new
/* where variant_name='Y:59022489:?>A'*/
$zigosity
=
$_GET
[
"zygosity"
];
$query
=
"SELECT variant_id "
.
"FROM shrine_ont.genomic_annotations_new "
.
"WHERE variant_name='"
.
$_GET
[
"variant_name"
]
.
"' AND "
.
"annotations ~* '"
.
"("
.
join
(
'|'
,
$zigosity
)
.
")'"
;
break
;
case
"annotation_and_zygosity"
:
//select variant_id
//from shrine_ont.genomic_annotations_new
//where annotations ~* '(Homozygous|Unknown);.*VARIANT_CLASS=DELETION'
$zigosity
=
$_GET
[
"zygosity"
];
$query
=
"SELECT variant_id "
.
"FROM shrine_ont.genomic_annotations_new "
.
"WHERE annotations ~* '"
.
"("
.
join
(
'|'
,
$zigosity
)
.
");.*"
.
$_GET
[
"annotation_name"
]
.
"="
.
$_GET
[
"annotation_value"
]
.
"'"
;
break
;
case
"old"
:
//select variant_id
//from shrine_ont.genomic_annotations
//where variant_annotations ->> 'Start_Position' = '5239176'
$query
=
"SELECT variant_id
FROM shrine_ont.genomic_annotations
WHERE variant_annotations ->> '"
.
$_GET
[
"annotation_name"
]
.
"' = '"
.
$_GET
[
"annotation_value"
]
.
"'"
;
break
;
default
:
echo
"Error: query type not recognized"
;
return
;
}
include
'sqlConnection.php'
;
$result
=
pg_query
(
$conn
,
$query
);
if
(!
$result
)
{
echo
"An error occurred while querying the database.
\n
"
;
exit
;
}
// In json format return both the panel number and the list of variants
echo
"{
\"
panel_number
\"
:"
.
$_GET
[
"panel_number"
]
.
",
\"
variants
\"
: "
;
$variantList
=
""
;
while
(
$row
=
pg_fetch_row
(
$result
))
{
$variantList
.=
"
\"
$row[0]
\"
,"
;
}
// drop the last comma
echo
"["
.
substr
(
$variantList
,
0
,
-
1
)
.
"]}"
;
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