Commit f0cdbdea authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

Added a 'flag' at Genebuilder request to allow them to switch off collection...

Added a 'flag' at Genebuilder request to allow them to switch off collection of NMD choices. They want to investigate these cases. Hacky job for a hacky script.
parent 2c09cad0
...@@ -9,6 +9,11 @@ ...@@ -9,6 +9,11 @@
# - Transcript length (longest) # - Transcript length (longest)
# - Translation length (longest) # - Translation length (longest)
# #
# A not so normal scenario is the choice of an NMD over an Ensembl protein
# coder. To emit these in all their glory, add NMD to the command line. e.g.
#
# perl reason_changes.pl logfile NMD
#
# If it was not one of these we will complain bitterly and you should # If it was not one of these we will complain bitterly and you should
# investigate. If it is a known reason after investigation, that is an # investigate. If it is a known reason after investigation, that is an
# allowed scenario, then code it into this script. # allowed scenario, then code it into this script.
...@@ -20,6 +25,7 @@ use warnings; ...@@ -20,6 +25,7 @@ use warnings;
use JSON; use JSON;
my $file = $ARGV[0]; my $file = $ARGV[0];
my $blurt = $ARGV[1] ;
if(! $file) { if(! $file) {
die "Was not given a file. Command is $0 PATH_TO_FILE"; die "Was not given a file. Command is $0 PATH_TO_FILE";
...@@ -77,7 +83,8 @@ sub compare { ...@@ -77,7 +83,8 @@ sub compare {
$old->[2] == 3 && #Old was an Ensembl/Havana transcript $old->[2] == 3 && #Old was an Ensembl/Havana transcript
$new->[2] == 2 && #New was E! Havana merged $new->[2] == 2 && #New was E! Havana merged
$old->[3] == 1 && #Old was a Protein Coding $old->[3] == 1 && #Old was a Protein Coding
$new->[3] == 2 #New was a "NMD" $new->[3] == 2 && #New was a "NMD"
$blurt !~ /nmd/i #User suppressing this test
) { ) {
$reason_key = 'havana_merge_nmd_over_e_coding'; $reason_key = 'havana_merge_nmd_over_e_coding';
} }
......
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