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ensembl-gh-mirror
ensembl
Commits
05219a6a
Commit
05219a6a
authored
20 years ago
by
Graham McVicker
Browse files
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now correctly replaces all 1-2bp introns with frameshifts
parent
8152d12a
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Changes
1
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1 changed file
misc-scripts/surgery/shortintrons2frameshifts.pl
+143
-70
143 additions, 70 deletions
misc-scripts/surgery/shortintrons2frameshifts.pl
with
143 additions
and
70 deletions
misc-scripts/surgery/shortintrons2frameshifts.pl
+
143
−
70
View file @
05219a6a
...
...
@@ -6,13 +6,14 @@ use Bio::EnsEMBL::DBSQL::DBAdaptor;
use
Getopt::
Long
;
use
POSIX
qw(ceil)
;
my
(
$host
,
$port
,
$user
,
$pass
,
$dbname
);
my
(
$host
,
$port
,
$user
,
$pass
,
$dbname
,
$testid
);
GetOptions
('
host=s
'
=>
\
$host
,
'
user=s
'
=>
\
$user
,
'
port=i
'
=>
\
$port
,
'
pass=s
'
=>
\
$pass
,
'
dbname=s
'
=>
\
$dbname
);
'
dbname=s
'
=>
\
$dbname
,
'
testid=i
'
=>
\
$testid
);
$port
||=
3306
;
...
...
@@ -51,30 +52,45 @@ my $ins_et_sth = $db->dbc->prepare(qq{INSERT INTO exon_transcript
transcript_id = ?,
rank = ?}
);
my
$upd_tl_sth
=
$db
->
dbc
->
prepare
(
qq{UPDATE translation
SET start_exon_id = ?,
end_exon_id = ?,
seq_start = ?,
seq_end = ?
WHERE translation_id = ?}
);
my
$sth
=
$db
->
dbc
->
prepare
(
qq{SELECT max(stable_id) FROM exon_stable_id}
);
$sth
->
execute
();
my
$ex_stable_id
=
$sth
->
fetchall_arrayref
->
[
0
]
->
[
0
];
$ex_stable_id
++
;
$sth
->
finish
();
$sth
=
$db
->
dbc
()
->
prepare
(
qq{SELECT t.gene_id,
MIN(IF(e1.seq_region_strand = 1,
e2.seq_region_start - e1.seq_region_end - 1,
e1.seq_region_start - e2.seq_region_end - 1)) AS intron_len
FROM exon e1, exon e2, exon_transcript et1, exon_transcript et2,
transcript t
WHERE et1.exon_id = e1.exon_id
AND et2.exon_id = e2.exon_id
AND et1.transcript_id = et2.transcript_id
AND et1.rank = et2.rank - 1
AND et1.transcript_id = t.transcript_id
GROUP BY t.gene_id
HAVING intron_len < 3}
);
if
(
!
$testid
)
{
$sth
=
$db
->
dbc
()
->
prepare
(
qq{SELECT t.gene_id,
MIN(IF(e1.seq_region_strand = 1,
e2.seq_region_start - e1.seq_region_end - 1,
e1.seq_region_start - e2.seq_region_end - 1)) AS intron_len
FROM exon e1, exon e2, exon_transcript et1, exon_transcript et2,
transcript t
WHERE et1.exon_id = e1.exon_id
AND et2.exon_id = e2.exon_id
AND et1.transcript_id = et2.transcript_id
AND et1.rank = et2.rank - 1
AND et1.transcript_id = t.transcript_id
GROUP BY t.gene_id
HAVING intron_len < 3}
);
$sth
->
execute
();
$sth
->
execute
();
}
my
@gene_ids
=
(
$testid
)
?
(
$testid
)
:
map
{
$_
->
[
0
]}
@
{
$sth
->
fetchall_arrayref
()};
my
$total_rows
=
$sth
->
rows
();
my
$total_rows
=
(
$testid
)
?
1
:
$sth
->
rows
();
my
$cur_row
=
0
;
my
$last_percent
=
undef
;
...
...
@@ -83,7 +99,7 @@ my $ea = $db->get_ExonAdaptor();
my
$aa
=
$db
->
get_AttributeAdaptor
();
print
STDERR
"
Merging exons and storing frameshifts
\n
";
while
(
my
$array
=
$sth
->
fetchrow_arrayref
()
)
{
foreach
my
$gene_id
(
@gene_ids
)
{
my
$percent
=
ceil
((
$cur_row
++
/
$total_rows
)
*
100
);
if
((
$percent
%
5
)
==
0
&&
...
...
@@ -92,90 +108,100 @@ while(my $array = $sth->fetchrow_arrayref()) {
print
STDERR
"
$percent
% complete
\n
";
}
my
$g
=
$ga
->
fetch_by_dbID
(
$
array
->
[
0
]
);
my
$g
=
$ga
->
fetch_by_dbID
(
$
gene_id
);
my
%old_exons
=
map
{
$_
->
hashkey
()
=>
$_
}
@
{
$g
->
get_all_Exons
()};
my
%new_exons
=
();
my
%tl_cdna_starts
;
my
%tl_cdna_ends
;
foreach
my
$tr
(
@
{
$g
->
get_all_Transcripts
})
{
# keep track of translation cdna coordinates before messing with transcript
my
(
$cdna_coding_start
,
$cdna_coding_end
);
if
(
$tr
->
translation
())
{
$cdna_coding_start
=
$tr
->
cdna_coding_start
();
$cdna_coding_end
=
$tr
->
cdna_coding_end
();
}
my
@frameshifts
;
# collect list of frameshifts
foreach
my
$intron
(
@
{
$tr
->
get_all_Introns
()})
{
push
(
@frameshifts
,
$intron
)
if
(
$intron
->
length
()
<
3
);
}
my
%seen_evidence
;
my
@exons
;
my
$fs
=
shift
(
@frameshifts
);
my
$merging_exon
;
my
$cdna_start
=
1
;
my
@exons
;
my
%seen_evidence
;
my
@old_exons
=
@
{
$tr
->
get_all_Exons
()};
while
(
@old_exons
)
{
my
$ex
=
shift
(
@old_exons
);
$cdna_start
+=
$ex
->
length
();
if
(
$fs
&&
$fs
->
prev_Exon
->
stable_id
()
eq
$ex
->
stable_id
())
{
$merging_exon
=
undef
;
# merge together exons which are seperated by frameshift introns
foreach
my
$ex
(
@
{
$tr
->
get_all_Exons
()})
{
while
(
$fs
&&
$fs
->
prev_Exon
->
stable_id
()
eq
$ex
->
stable_id
())
{
# this exon has a frameshift, so merge it with next exon
# and any subsequent exons serperated only by frameshifts
# was the previous exon seperated from this one by a frameshift intron?
if
(
$fs
&&
$fs
->
next_Exon
()
->
stable_id
()
eq
$ex
->
stable_id
())
{
if
(
!
$merging_exon
)
{
$merging_exon
=
{};
%
{
$merging_exon
}
=
%$ex
;
bless
$merging_exon
,
ref
(
$ex
);
push
@exons
,
$merging_exon
;
# merge this exon with the previous one
if
(
$ex
->
strand
()
==
1
)
{
$exons
[
$#exons
]
->
end
(
$ex
->
end
());
}
else
{
$exons
[
$#exons
]
->
start
(
$ex
->
start
());
}
%seen_evidence
=
();
# merge supporting evidence
foreach
my
$sf
(
@
{
$ex
->
get_all_supporting_features
()})
{
if
(
!
$seen_evidence
{
ref
(
$sf
)
.
'
:
'
.
$sf
->
dbID
()})
{
$ex
->
add_supporting_feature
(
$sf
);
$seen_evidence
{
ref
(
$sf
.
'
:
'
.
$sf
->
dbID
())}
=
1
;
}
}
if
(
$merging_exon
->
strand
()
==
1
)
{
$merging_exon
->
end
(
$fs
->
next_Exon
()
->
end
());
}
else
{
$merging_exon
->
start
(
$fs
->
next_Exon
()
->
start
());
# store frameshift as transcript attrib
my
$seqed
=
Bio::EnsEMBL::
SeqEdit
->
new
(
-
CODE
=>
'
_rna_edit
',
-
NAME
=>
'
RNA Edit
',
-
DESC
=>
'
Post transcriptional RNA edit
',
-
START
=>
$cdna_start
,
-
END
=>
$cdna_start
+
$fs
->
length
()
-
1
,
-
ALT_SEQ
=>
'');
$aa
->
store_on_Transcript
(
$tr
,
[
$seqed
->
get_Attribute
]);
# adjust cdna coordinates for frameshifted basepairs
if
(
$tr
->
translation
)
{
if
(
$cdna_coding_start
>=
$cdna_start
)
{
$cdna_coding_start
+=
$fs
->
length
();
}
# merge supporting evidence
foreach
my
$ev
(
@
{
$ex
->
get_all_supporting_features
()})
{
if
(
!
$seen_evidence
{
$ev
->
dbID
()})
{
$merging_exon
->
add_supporting_features
(
$ev
);
$seen_evidence
{
$ev
->
dbID
()}
=
1
;
}
if
(
$cdna_coding_end
>=
$cdna_start
)
{
$cdna_coding_end
+=
$fs
->
length
();
}
# store frameshift as transcript attrib
my
$seqed
=
Bio::EnsEMBL::
SeqEdit
->
new
(
-
CODE
=>
'
_rna_edit
',
-
NAME
=>
'
RNA Edit
',
-
DESC
=>
'
Post transcriptional RNA edit
',
-
START
=>
$cdna_start
,
-
END
=>
$cdna_start
+
$fs
->
length
()
-
1
,
-
ALT_SEQ
=>
'');
$aa
->
store_on_Transcript
(
$tr
,
[
$seqed
->
get_Attribute
]);
# take this frameshift and the next exon
# (which was merged into the current exon) off the list
$fs
=
shift
(
@frameshifts
);
$ex
=
shift
(
@old_exons
);
$cdna_start
+=
$ex
->
length
();
}
}
else
{
# this exon does not have a frameshift so just add it to the list
$cdna_start
+=
$fs
->
length
();
# look at the next frameshift
$fs
=
shift
(
@frameshifts
);
}
else
{
push
@exons
,
$ex
;
%seen_evidence
=
();
foreach
my
$sf
(
@
{
$ex
->
get_all_supporting_features
()})
{
$seen_evidence
{
ref
(
$_
)
.
'
:
'
.
$_
->
dbID
()}
=
1
;
}
}
$cdna_start
+=
$ex
->
length
();
}
# rebuild transcript from new set of exons
$tr
->
flush_Exons
();
foreach
my
$ex
(
@exons
)
{
$new_exons
{
$ex
->
hashkey
}
=
$ex
;
$tr
->
add_Exon
(
$ex
);
}
$tl_cdna_starts
{
$tr
->
dbID
()}
=
$cdna_coding_start
;
$tl_cdna_ends
{
$tr
->
dbID
()}
=
$cdna_coding_end
;
}
# determine which exons can be deleted
...
...
@@ -200,6 +226,7 @@ while(my $array = $sth->fetchrow_arrayref()) {
}
}
# update the transcript composition by updating the exon transcript table
foreach
my
$tr
(
@
{
$g
->
get_all_Transcripts
()})
{
$del_et_sth
->
execute
(
$tr
->
dbID
());
...
...
@@ -218,11 +245,57 @@ while(my $array = $sth->fetchrow_arrayref()) {
$rank
++
;
}
}
# update the translations to use the new exons
foreach
my
$tr
(
@
{
$g
->
get_all_Transcripts
()})
{
my
$tl
=
$tr
->
translation
();
next
if
(
!
$tl
);
my
$tl_start
=
$tl_cdna_starts
{
$tr
->
dbID
()};
my
$tl_end
=
$tl_cdna_ends
{
$tr
->
dbID
()};
foreach
my
$ex
(
@
{
$tr
->
get_all_Exons
()})
{
if
(
$tl_start
>
0
&&
$tl_start
<=
$ex
->
length
())
{
$tl
->
start_Exon
(
$ex
);
$tl
->
start
(
$tl_start
);
}
if
(
$tl_end
>
0
&&
$tl_end
<=
$ex
->
length
())
{
$tl
->
end_Exon
(
$ex
);
$tl
->
end
(
$tl_end
);
}
$tl_start
-=
$ex
->
length
();
$tl_end
-=
$ex
->
length
();
}
my
(
$start_ex_id
,
$end_ex_id
);
# use consolidated exon ids. Exons may have been duplicated across
# multiple transcripts but only one has been stored and had id set.
if
(
$old_exons
{
$tl
->
start_Exon
->
hashkey
()})
{
$start_ex_id
=
$old_exons
{
$tl
->
start_Exon
->
hashkey
()}
->
dbID
();
}
else
{
$start_ex_id
=
$new_exons
{
$tl
->
start_Exon
->
hashkey
()}
->
dbID
();
}
if
(
$old_exons
{
$tl
->
end_Exon
->
hashkey
()})
{
$end_ex_id
=
$old_exons
{
$tl
->
end_Exon
->
hashkey
()}
->
dbID
();
}
else
{
$end_ex_id
=
$new_exons
{
$tl
->
end_Exon
->
hashkey
()}
->
dbID
();
}
$upd_tl_sth
->
execute
(
$start_ex_id
,
$end_ex_id
,
$tl
->
start
(),
$tl
->
end
(),
$tl
->
dbID
());
}
}
$del_et_sth
->
finish
();
$ins_et_sth
->
finish
();
$sth
->
finish
();
$upd_tl_sth
->
finish
();
print
STDERR
"
\n
All Done.
\n
";
...
...
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