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ensembl-gh-mirror
ensembl
Commits
0dfcf9d9
Commit
0dfcf9d9
authored
12 years ago
by
Kieron Taylor
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parent
4189b37d
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1 changed file
misc-scripts/assembly/check_mapping.pl
+21
-4
21 additions, 4 deletions
misc-scripts/assembly/check_mapping.pl
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21 additions
and
4 deletions
misc-scripts/assembly/check_mapping.pl
+
21
−
4
View file @
0dfcf9d9
...
...
@@ -21,6 +21,10 @@ Required arguments:
--altdbname=NAME alternative database NAME
--altassembly=ASSEMBLY alternative assembly version ASSEMBLY
--nolog outside of a webserver environment,
logging needs to be handled manually.
Use in conjunction with shell redirects.
Optional arguments:
--althost=HOST alternative databases host HOST
...
...
@@ -63,10 +67,6 @@ for the details.
This code is distributed under an Apache style licence:
Please see http://www.ensembl.org/code_licence.html for details
=head1 AUTHOR
Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
=head1 CONTACT
Please post comments/questions to the Ensembl development list
...
...
@@ -91,6 +91,8 @@ use Getopt::Long;
use
Pod::
Usage
;
use
Bio::EnsEMBL::Utils::
ConversionSupport
;
use
Algorithm::
Diff
qw(diff)
;
$|
=
1
;
my
$support
=
new
Bio::EnsEMBL::Utils::
ConversionSupport
(
$SERVERROOT
);
...
...
@@ -150,6 +152,8 @@ my $A_sa = $A_dba->get_SliceAdaptor;
$support
->
log
("
Looping over toplevel seq_regions...
\n\n
");
my
@global_diff_bins
;
foreach
my
$chr
(
$support
->
sort_chromosomes
)
{
$support
->
log_stamped
("
Toplevel seq_region
$chr
...
\n
",
1
);
...
...
@@ -207,6 +211,11 @@ foreach my $chr ($support->sort_chromosomes) {
$support
->
log
("
Alt:
$A_sub_seq
\n\n
",
3
);
$i
++
;
my
@Ref
=
split
(
//
,
$R_seq
);
my
@Alt
=
split
(
//
,
$A_seq
);
my
@diffs
=
diff
(
\
@Ref
,
\
@Alt
);
$global_diff_bins
[
scalar
(
@diffs
)]
++
;
}
$k
++
;
...
...
@@ -221,6 +230,14 @@ foreach my $chr ($support->sort_chromosomes) {
$support
->
log_stamped
("
Done.
\n\n
",
1
);
}
$support
->
log
("
Summary of changes across all chromosomes
\n\n
",
1
);
$support
->
log
("
|Bin |Frequency
\n
",
2
);
for
(
my
$bin
=
0
;
$bin
<
scalar
(
@global_diff_bins
);
$bin
++
)
{
if
(
defined
(
$global_diff_bins
[
$bin
]))
{
$support
->
log
("
|
$bin
|
$global_diff_bins
[
$bin
]
\n
");
}
}
# finish logfile
$support
->
finish_log
;
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