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ensembl-gh-mirror
ensembl
Commits
f9c20a07
Commit
f9c20a07
authored
Oct 19, 2011
by
Daniel Barrell
Browse files
WGA/Projection used for CHIMP2.1.4
parent
3d11fdf0
Changes
2
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2 changed files
with
8 additions
and
4 deletions
+8
-4
modules/Bio/EnsEMBL/BaseAlignFeature.pm
modules/Bio/EnsEMBL/BaseAlignFeature.pm
+1
-0
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+7
-4
No files found.
modules/Bio/EnsEMBL/BaseAlignFeature.pm
View file @
f9c20a07
...
...
@@ -715,6 +715,7 @@ sub _parse_features {
my
$query_p_length
=
sprintf
"
%.0f
",
(
$length
/
$query_unit
);
my
$hit_p_length
=
sprintf
"
%.0f
",
(
$hlength
*
$hit_unit
);
if
(
$query_p_length
!=
$hit_p_length
)
{
print
"
$query_p_length
(query_p_length) !=
$hit_p_length
(hit_p_length)
\n
";
throw
(
"
Feature lengths not comparable Lengths:
"
.
$length
.
"
"
.
$hlength
.
"
Ratios:
"
.
$query_unit
.
"
"
.
$hit_unit
);
...
...
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
View file @
f9c20a07
...
...
@@ -296,10 +296,10 @@ sub _fetch_seq {
my
$min
=
(
$i
<<
$SEQ_CHUNK_PWR
)
+
1
;
#print STDERR "SELECT SUBSTRING(d.sequence, $min, $SEQ_CHUNK_PWR FROM dna d WHERE d.seq_region_id = $seq_region_id;\n";
$sth
->
bind_param
(
1
,
$min
,
SQL_INTEGER
);
$sth
->
bind_param
(
2
,
1
<<
$SEQ_CHUNK_PWR
,
SQL_INTEGER
);
$sth
->
bind_param
(
3
,
$seq_region_id
,
SQL_INTEGER
);
$sth
->
execute
();
$sth
->
bind_columns
(
\
$tmp_seq
);
$sth
->
fetch
();
...
...
@@ -307,15 +307,18 @@ sub _fetch_seq {
# always give back uppercased sequence so it can be properly softmasked
$entire_seq
.=
uc
(
$tmp_seq
);
$cache
->
{"
$seq_region_id
:
$i
"}
=
$tmp_seq
;
$cache
->
{"
$seq_region_id
:
$i
"}
=
uc
(
$tmp_seq
)
;
}
}
# return only the requested portion of the entire sequence
my
$min
=
(
$chunk_min
<<
$SEQ_CHUNK_PWR
)
+
1
;
my
$max
=
(
$chunk_max
+
1
)
<<
$SEQ_CHUNK_PWR
;
#my $max = ( $chunk_max + 1 ) << $SEQ_CHUNK_PWR;
# print STDERR "start: $start min: $min length: $length\n";
# print STDERR "ENTIRE SEQ START \n$entire_seq\nENTIRE_SEQ_END\n";
# print STDERR " substr( $start - $min, $length )\n";
my
$seq
=
substr
(
$entire_seq
,
$start
-
$min
,
$length
);
#print "$seq\n";
return
\
$seq
;
}
else
{
...
...
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