From 7fd559e5ce3733d812b4be7d2f294a9c09061f6c Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Wed, 27 Jan 2016 17:06:23 +0000
Subject: [PATCH] Remove egregious spelling and comments. Also fix some
tabulation.
---
.../XrefMapper/ProcessPrioritys.pm | 61 ++++++++-----------
1 file changed, 26 insertions(+), 35 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
index 10f41b4cd9..07c6007516 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
@@ -40,7 +40,7 @@ use IPC::Open3;
#
# 3) for each of the source names
# set ox_status to 'FAILED_PRIORITY' for those not the best match
-# Also do this fro its depenedents
+# Also do this for its depenedents
#
sub new {
@@ -84,7 +84,7 @@ sub process {
my @names = $self->get_priority_names();
- print "The foillowing will be processed as priority xrefs\n" if($self->verbose);
+ print "The following will be processed as priority xrefs\n" if($self->verbose);
foreach my $name (@names){
print "\t$name\n" if($self->verbose);
}
@@ -92,10 +92,6 @@ sub process {
my $update_ox_sth = $self->xref->dbc->prepare('update object_xref set ox_status = "FAILED_PRIORITY" where object_xref_id = ?');
my $update_x_sth = $self->xref->dbc->prepare("update xref set dumped = 'NO_DUMP_ANOTHER_PRIORITY' where xref_id = ?");
- #
- # Change of tact here to make the sql easier...
- #
-
# 1) Set to failed all those that have no object xrefs.
my $f_sql =(<<FSQL);
@@ -179,7 +175,7 @@ SEQCP
my @gone;
while($sth->fetch){
if($last_acc eq $acc){
- if($xref_id != $best_xref_id){
+ if($xref_id != $best_xref_id){
if ($xref_id == $last_xref_id) {
$seen = 1;
} else {
@@ -197,7 +193,7 @@ SEQCP
$best_ox_sth->fetch();
$idx_copy_sth->execute($query_identity, $target_identity, $hit_start, $hit_end, $translation_start, $translation_end, $cigar_line, $score, $evalue, $best_object_xref_id);
}
- if($status eq "DUMP_OUT"){
+ if($status eq "DUMP_OUT"){
$update_ox_sth->execute($object_xref_id);
## If it is the first time processing this xref_id, also process dependents and update status
if (!$seen) {
@@ -207,33 +203,33 @@ SEQCP
$self->process_dependents($xref_id, $best_xref_id, $object_type, \@best_ensembl_id);
}
}
- else{
- $update_x_sth->execute($xref_id);
- }
- } else {
+ else{
+ $update_x_sth->execute($xref_id);
+ }
+ } else {
## There might be several mappings for the best priority
push @best_ensembl_id, $ensembl_id;
}
- if(@gone){ #best priority failed so anothre one now found so set dumped;
- if($last_name eq $acc){
- foreach my $d (@gone){
- $update_x_sth->execute($d);
- }
- }
- }
+ if(@gone){ #best priority failed so another one now found so set dumped;
+ if($last_name eq $acc){
+ foreach my $d (@gone){
+ $update_x_sth->execute($d);
+ }
+ }
+ }
}
else{ # NEW
- if($status eq "DUMP_OUT"){
- $last_acc = $acc;
- $best_xref_id = $xref_id;
- @best_ensembl_id = ($ensembl_id);
- if(@gone and $last_name eq $acc){
- foreach my $d (@gone){
- $update_x_sth->execute($d);
- }
- @gone=();
- }
- }
+ if($status eq "DUMP_OUT"){
+ $last_acc = $acc;
+ $best_xref_id = $xref_id;
+ @best_ensembl_id = ($ensembl_id);
+ if(@gone and $last_name eq $acc){
+ foreach my $d (@gone){
+ $update_x_sth->execute($d);
+ }
+ @gone=();
+ }
+ }
else{
if($last_name eq $acc){
push @gone, $xref_id; }
@@ -255,11 +251,6 @@ SEQCP
$idx_copy_sth->finish;
$syn_copy_sth->finish;
-
-# We want to make sure that if a priority xref is NOT MAPPEd then we only
-
-
-
$sth = $self->xref->dbc->prepare("insert into process_status (status, date) values('prioritys_flagged',now())");
$sth->execute();
$sth->finish;
--
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