Changeset 235

Timestamp:

07/14/09 23:23:44 (4 months ago)

Author:

cholt

Message:

fixed for abinit to pred_gff

Files:

• bin/maker2zff.pl (modified) (4 diffs)
• lib/GI.pm (modified) (1 diff)
• lib/maker/auto_annotator.pm (modified) (11 diffs)

bin/maker2zff.pl

@@ -46 +46 @@
-my %exons = ();
-my %hc = ();
+my %bad = ();
-my %seq = ();
-
@@ -62 +63 @@
-
-#### Go through the GFF file and determine which genes are HC  ####
+#### This step must finish before any output is produced since ####
+#### featues can be out of order ####
+
+my %index; #used to replace long maker names that mess up snap
+my $count = 0;
-
-foreach my $file (@files) {
@@ -96 +102 @@
-                my $ishc = is_hc($qi, $AED);
-                if ($ishc == 1 ) {
-$hc{$id} = 1
+push(@{$hc{$seqid}}, $id)
-                }
-            }elsif ($tag eq "CDS" && $source eq "maker") {
-                my $parent = $annotation{'Parent'};
-
-
-
-
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+
-                }
-
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+
-            }
-        }
-    }
-}
+
+#### Now filter out anything thats not high quality ####
-
-#### Print out the exon locations of the HC genes ####
@@ -116 +130 @@
-open DNA, ">$outfile\.dna" or die $!;
-
-
-
+
-    print ZFF ">",$seqid,"\n";
-    print DNA ">",$seqid,"\n",$seq{$seqid},"\n";
-
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-        }
-    }
-}
+
+close(ZFF);
+close(DNA);
-
-################## Subroutines ###################

lib/GI.pm

@@ -2316 +2316 @@
-   foreach my $p (@predictors) {
-       if ($p !~ /^snap$|^augustus$|^est2genome$|^fgenesh$/ &&
-abinit
+pred_gff
-           ) {
-           $error .= "ERROR: Invalid predictor defined: $p\n".
-snap
-genemark, augustus, fgenesh, and abinit
+pred_gff
+snap, genemark, augustus, and fgenesh
-       }
-       else {

lib/maker/auto_annotator.pm

@@ -637 +637 @@
-    }
-    
-
+ (includes est2genome)
-    foreach my $prdr (@{$CTL_OPTIONS->{_predictor}}){
-abinit' || $prdr eq 'genemark
+pred_gff
-        print STDERR "Producing $prdr hint based annotations\n" unless($main::quiet);
-        
@@ -673 +673 @@
-                            $v_seq_ref,
-                            $def,
-
+ #all abinits not just pref_gff
-                            $predictions,
-                            $CTL_OPTIONS
@@ -683 +683 @@
-                                   $chunk_number,
-                                   $build,
-
+ #all abinits not_just pred_gff
-                                   $the_void,
-                                   $CTL_OPTIONS
-                                   );
-
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-    
-    add_abAED(\%annotations);
-
-    #fill genemark hint based with abinits since hints do not work
-    #but only if not using abinits already
-    if((grep {/^genemark$/} @{$CTL_OPTIONS->{_predictor}}) &&
-       (! grep {/^abinit$/} @{$CTL_OPTIONS->{_predictor}})
-      ){
-        foreach my $g (@$all_ab){
-            if($g->{algorithm} =~ /^genemark_masked$/i){
-                push(@{$annotations{'genemark'}}, $g);
-            }
-            elsif($CTL_OPTIONS->{_no_mask} && $g->{algorithm} =~ /^genemark$/i){
-                push(@{$annotations{'genemark'}}, $g);
-            }
-        }
-
-    }
-
-    return \%annotations;
@@ -789 +797 @@
-    #collect all no UTR base models to get abAED
-    foreach my $p (keys %$annotations){
+        next if ($p eq 'abinit'); #these are redundant inside predictor type
-        foreach my $g (@{$annotations->{$p}}){
-            if($g->{g_strand} == 1){
@@ -851 +860 @@
-    my @p_keepers;
-    my @m_keepers;
-
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-        #set up lists for plus and minus strands as well as possible mergers
-        #predictor types are processed in the order given by control files
@@ -890 +911 @@
-        push(@m_keepers, @$m_list);
-    }
-    elsif(@{$CTL_OPTIONS->{_predictor}}){
-        my $key = $CTL_OPTIONS->{_predictor}->[0];
-        foreach my $g (@{$annotations->{$key}}){
-            if($g->{g_strand} == 1){
-                push(@p_keepers, $g) if($g->{AED} < 1  || $key eq 'model_gff');
-            }
-            elsif($g->{g_strand} == -1){
-                push(@m_keepers, $g) if($g->{AED} < 1  || $key eq 'model_gff');
-            }
-        }
-    }
-
-    #remove CDS competition on opposite strand
@@ -1206 +1216 @@
-            next;
-        }
-
-        #------genemark does not have hints enabled 
-        return [] if ($predictor eq 'genemark');
-        
-        #------est2genome
@@ -1224 +1231 @@
-            next;
-        }
+
+        #------genemark does not have hints enabled 
+        return [] if ($predictor eq 'genemark');
-        
-        #------default hint based behavior
@@ -1544 +1554 @@
-   }
-   
-
+r
-   my @keepers;
-   foreach my $c (@{$careful_clusters}) {
@@ -1850 +1860 @@
-#that don't overlap maker's final annotation set. The non-overlapping
-#set is filtered using abAED so that they don't overlap each other.
+#Only masked ab inits are considered (otherwise I get a lot of revere
+#transcriptase genes).  Unmasked are allowed when there is no masking
+#performed.
-
-sub get_non_overlaping_abinits {
@@ -1874 +1887 @@
-   }
-
-
+ (only masked unless I'm not masking)
-   my @p_ab;
-   my @m_ab;