adding check against inadvertently log-2 transformed splicing fold ch…

…ange column in HBADEALS file.

isopret-cli/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.1</version>
+        <version>1.3.2</version>
     </parent>
 
     <artifactId>isopret-cli</artifactId>

isopret-core/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.1</version>
+        <version>1.3.2</version>
     </parent>
 
     <artifactId>isopret-core</artifactId>

isopret-core/src/main/java/org/jax/isopret/core/impl/rnaseqdata/RnaSeqResultLine.java

@@ -46,5 +46,16 @@ public boolean isIsoform() {
     }
 
 
+    /**
+     * Check for a common user error -- the splice fold change is "raw" (not logarithm), which the expression
+     * fold change is log2. These are separate lines in the HBADEALS result file.
+     * @return true if the line does not have negative and thus potentially log2-transformed splicing value
+     */
+    public boolean isValid() {
+        final double EPSILON = 0.001;
+        return !isIsoform() || !((expFC + EPSILON) < 0);
+    }
+
+
 
 }

isopret-core/src/main/java/org/jax/isopret/core/impl/rnaseqdata/RnaSeqResultsParser.java

@@ -11,7 +11,12 @@
 import java.util.*;
 
 /**
- * Parse the HBA-DEALS output file, e.g.,
+ * Parse the HBA-DEALS output file.
+ * The HBA-DEALS output file contains 4 columns. The first column is the gene name, the second is the transcript name, the third is the fold change,
+ * and the fourth is 1-probability of differential expression or proportion(splicing), which is the posterior error probability (PEP).
+ * Entries that refer to expression have ‘Expression’ in their second column. If isoform.level is FALSE, entries that refer to differential
+ * splicing of the gene will have ‘Splicing’ in their second column entry.
+ * The fold change for expression is given as log2 fold change, and for splicing as fold change.
  * <p>
  * Gene	Isoform	ExplogFC/FC	P
  * ENSG00000160710	Expression	1.54770825394965	0
@@ -87,7 +92,12 @@ private Map<AccessionNumber, GeneResult> parseResults(BufferedReader br) throws
             }
 
         int found_symbol = 0;
+        int invalid_lines = 0;
         for (RnaSeqResultLine hline : lines) {
+            if (! hline.isValid()) {
+                invalid_lines++;
+                continue;
+            }
             AccessionNumber ensgAccession = hline.geneAccession(); // if we cannot find symbol, just show the accession
             if (hgncMap.containsKey(ensgAccession)) {
                 GeneModel model = hgncMap.get(ensgAccession);
@@ -114,6 +124,11 @@ private Map<AccessionNumber, GeneResult> parseResults(BufferedReader br) throws
         if (! unfound.isEmpty()) {
             LOGGER.info("Could not find symbols for {} accessions.", unfound.size());
         }
+        if (invalid_lines > 0) {
+            String errmsg = String.format("%d invalid lines (splicing fold change negative-but only expr values should be log2). Fix before continuing.",
+                    invalid_lines);
+            throw new IsopretRuntimeException(errmsg);
+        }
         return resultsMap;
     }
 
@@ -146,12 +161,4 @@ public static Map<AccessionNumber, GeneResult> parse(File file,
         return parser.ensgAcc2geneResultMap;
     }
 
-
-    private Map<AccessionNumber, GeneResult> getEnsgAcc2geneResultMap() {
-        return this.ensgAcc2geneResultMap;
-    }
-
-
-
-
 }

isopret-data/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.1</version>
+        <version>1.3.2</version>
     </parent>
 
     <artifactId>isopret-data</artifactId>

isopret-exception/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.1</version>
+        <version>1.3.2</version>
     </parent>
 
     <artifactId>isopret-exception</artifactId>

isopret-gui/pom.xml

@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.1</version>
+        <version>1.3.2</version>
     </parent>
 
     <artifactId>isopret-gui</artifactId>

isopret-io/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.1</version>
+        <version>1.3.2</version>
     </parent>
     <packaging>jar</packaging>
     <artifactId>isopret-io</artifactId>

pom.xml

@@ -10,7 +10,7 @@
     </parent>
     <groupId>org.jax.isopret</groupId>
     <artifactId>isopret</artifactId>
-    <version>1.3.1</version>
+    <version>1.3.2</version>
     <modules>
         <module>isopret-core</module>
         <module>isopret-cli</module>