From 521118ea44faf50ec49b2f8daaf580da9daf1d17 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 21 Aug 2013 14:13:56 +0100
Subject: [PATCH] add check for ID prefix in gene models
---
uk/ac/sanger/artemis/io/ValidateFeature.java | 56 +++++++++++++++++++-
1 file changed, 55 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/io/ValidateFeature.java b/uk/ac/sanger/artemis/io/ValidateFeature.java
index eb3551cdf..202710694 100644
--- a/uk/ac/sanger/artemis/io/ValidateFeature.java
+++ b/uk/ac/sanger/artemis/io/ValidateFeature.java
@@ -33,6 +33,7 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.Vector;
+import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.swing.JOptionPane;
@@ -71,6 +72,7 @@ public class ValidateFeature
//##sequence-region seqid start end
private static Pattern HEADER_SEQ_REGION = Pattern.compile("##sequence-region \\S+ \\d+ \\d+");
private static Pattern CAPITAL_START = Pattern.compile("^[A-Z]+\\S*");
+ private static Pattern ID_PREFIX = Pattern.compile("^[^.:]+");
private static String[] RESERVED_TAGS =
{ "ID", "Name", "Alias", "Parent",
@@ -133,7 +135,8 @@ public class ValidateFeature
showFeatureList(STRAND_PREDICATE, "Gene Strand Errors", grp, sel, gotoSrc, plotGrp);
showFeatureList(BOUNDARY_PREDICATE, "Gene Boundary Errors", grp, sel, gotoSrc, plotGrp);
showFeatureList(COMPLETE_GENE_MODEL_PREDICATE, "Incomplete Gene Model", grp, sel, gotoSrc, plotGrp);
- showFeatureList(PARTIAL_PREDICATE, "Partial Settings", grp, sel, gotoSrc, plotGrp);
+ showFeatureList(PARTIAL_PREDICATE, "Check Partial Settings", grp, sel, gotoSrc, plotGrp);
+ showFeatureList(ID_PREDICATE, "Check ID Settings", grp, sel, gotoSrc, plotGrp);
}
showFeatureList(INTERNAL_STOP, "Internal Stop Codons", grp, sel, gotoSrc, plotGrp);
@@ -219,6 +222,12 @@ public class ValidateFeature
pass = false;
report.put("Partial settings not consistent", Level.FATAL);
}
+
+ if(!isIdPrefixConsistent(gffFeature))
+ {
+ pass = false;
+ report.put("Prefix of ID attribute not consistent within gene model", Level.FATAL);
+ }
}
if( (entryGrp == null || !GeneUtils.isDatabaseEntry(entryGrp)) && !isCDSPhaseOK(gffFeature))
@@ -544,6 +553,41 @@ public class ValidateFeature
return true;
}
+ /**
+ * Test if the ID GFF3 attribute prefix is consistent within a gene model
+ * @param gffFeature
+ * @return true if the prefix is the same within the gene model features
+ */
+ private static boolean isIdPrefixConsistent(final GFFStreamFeature gffFeature)
+ {
+ final ChadoCanonicalGene gene = gffFeature.getChadoGene();
+ if(gene == null)
+ return true;
+
+ try
+ {
+ if(gffFeature.getKey().getKeyString().endsWith("gene"))
+ return (gene.getGene().getQualifierByName("ID") != null);
+
+ if(gene.getGene().getQualifierByName("ID") == null)
+ return true;
+ if(gffFeature.getQualifierByName("ID") == null)
+ return false;
+
+ String id = gene.getGene().getQualifierByName("ID").getValues().elementAt(0);
+ final Matcher m = ID_PREFIX.matcher(id);
+ if(m.matches())
+ {
+ id = gffFeature.getQualifierByName("ID").getValues().elementAt(0);
+ return id.startsWith( m.group() );
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return true;
+ }
/**
* The phase is REQUIRED for all CDS features.
@@ -912,6 +956,16 @@ public class ValidateFeature
}
};
+ private static FeaturePredicate ID_PREDICATE = new FeaturePredicate()
+ {
+ public boolean testPredicate(uk.ac.sanger.artemis.Feature feature)
+ {
+ if( isIdPrefixConsistent((GFFStreamFeature) feature.getEmblFeature() ))
+ return false;
+ return true;
+ }
+ };
+
private FeaturePredicate INTERNAL_STOP = new FeaturePredicate()
{
public boolean testPredicate(uk.ac.sanger.artemis.Feature feature)
--
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