diff --git a/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm b/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm index 0788628cf7c348e0ab0d23d264851d721def9b5e..c81a9d1e93e7ad8cfcafa2a53ab28fb971df3cc6 100644 --- a/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm +++ b/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm @@ -37,6 +37,7 @@ sub new { bless $self,$class; $self->core($mapper->core); $self->xref($mapper->xref); + $self->verbose($mapper->verbose); return $self; } @@ -131,7 +132,7 @@ SQL $internal_id = $stable_id; } else{ - print "Could not find stable id $stable_id in table to get the internal id hence ignoring!!!\n" if($self->mapper->verbose); + print "Could not find stable id $stable_id in table to get the internal id hence ignoring!!!\n" if($self->verbose); $err_count++; next; } @@ -176,9 +177,9 @@ SQL } $sth->finish; if($duplicate_direct_count or $duplicate_dependent_count){ - print "duplicate entrys ignored for $duplicate_direct_count direct xrefs and $duplicate_dependent_count dependent xrefs\n" if($self->mapper->verbose); + print "duplicate entrys ignored for $duplicate_direct_count direct xrefs and $duplicate_dependent_count dependent xrefs\n" if($self->verbose); } - if($err_count or $self->mapper->verbose){ + if($err_count or $self->verbose){ print STDERR $count." direct_xrefs added to ensembl ".$table."s BUT $err_count stable ids could not be found\n"; } } diff --git a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm index 4dd8ce76bc8ddd1b6b4140cdb2d1fd7a1b270a6c..4c1819007e63585b41656308d2c9dfe416b2cc2a 100644 --- a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm +++ b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm @@ -14,6 +14,7 @@ sub new { bless $self,$class; $self->core($mapper->core); $self->xref($mapper->xref); + $self->verbose($mapper->verbose); return $self; } @@ -21,7 +22,7 @@ sub new { sub process{ my $self = shift; - print "Writing InterPro\n" if($self->mapper->verbose); + print "Writing InterPro\n" if($self->verbose); my( $ipro_count, $xref_count, $oxref_count, $goxref_count ) = (0,0,0,0); my $object_xref_id; @@ -93,11 +94,11 @@ sub process{ $sth->finish(); - print "\n".$dup." already existed\n\n" if($self->mapper->verbose); + print "\n".$dup." already existed\n\n" if($self->verbose); - print(" Wrote $ipro_count interpro table entries\n") if($self->mapper->verbose); - print(" including $oxref_count object xrefs, \n") if($self->mapper->verbose); - print(" and $goxref_count go xrefs\n") if($self->mapper->verbose); + print(" Wrote $ipro_count interpro table entries\n") if($self->verbose); + print(" including $oxref_count object xrefs, \n") if($self->verbose); + print(" and $goxref_count go xrefs\n") if($self->verbose); # foreach my $key (keys %added){ # print "id= $key has ".$added{$key}. " object xrefs added\n"; # } diff --git a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm index 6cabf6d0967dd92bb8cfb139b7e9adec076eb3c7..3ffaa4763804cd9c46cb8ad4787f8102892ee0cc 100644 --- a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm +++ b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm @@ -32,6 +32,7 @@ sub new { bless $self,$class; # $self->core($mapper->core); $self->xref($mapper->xref); + $self->verbose($mapper->verbose); return $self; } @@ -65,9 +66,9 @@ sub process { my @names = $self->get_priority_names(); - print "The foillowing will be processed as priority xrefs\n" if($self->mapper->verbose); + print "The foillowing will be processed as priority xrefs\n" if($self->verbose); foreach my $name (@names){ - print "\t$name\n" if($self->mapper->verbose); + print "\t$name\n" if($self->verbose); } my $update_ox_sth = $self->xref->dbc->prepare('update object_xref set ox_status = "FAILED_PRIORITY" where object_xref_id = ?');