Updates to annotator by genomic change (#191)

- Make TUMOR_SEQ_ALLELE1 column optional, it is usually the reference allele
- Support chr prefix for chromosome

AnnotatorCore.py

@@ -202,7 +202,7 @@ def setsampleidsfileterfile(f):
 GC_VAR_ALLELE_1_HEADER = 'TUMOR_SEQ_ALLELE1'
 GC_VAR_ALLELE_2_HEADER = 'TUMOR_SEQ_ALLELE2'
 GENOMIC_CHANGE_HEADERS = [GC_CHROMOSOME_HEADER, GC_START_POSITION_HEADER, GC_END_POSITION_HEADER, GC_REF_ALLELE_HEADER,
-                          GC_VAR_ALLELE_1_HEADER, GC_VAR_ALLELE_2_HEADER]
+                          GC_VAR_ALLELE_2_HEADER]
 
 # columns for structural variant annotation
 SV_GENEA_HEADER = ['SITE1_GENE', 'GENEA', 'GENE1', 'SITE1_HUGO_SYMBOL']
@@ -1504,13 +1504,17 @@ def getimplications(oncokbdata, implication_type, levels, implications):
 
 class GenomicChangeQuery:
     def __init__(self, chromosome, start, end, ref_allele, var_allele, cancertype, reference_genome=None):
+        if chromosome is not None:
+            chromosome = chromosome.strip()
+            if chromosome.startswith('chr'):
+                chromosome = chromosome[3:]
         self.genomicLocation = ','.join([chromosome, start, end, ref_allele, var_allele])
         self.tumorType = cancertype
         if reference_genome is not None:
             self.referenceGenome = reference_genome.value
 
     def __repr__(self):
-        return " ".join([self.genomicLocation, self.tumorType, self.referenceGenome])
+        return " ".join([self.genomicLocation, self.tumorType])
 
 
 class CNAQuery:

README.md

@@ -67,10 +67,19 @@ OncoKB™ MafAnnotator supports annotating the alteration with HGVSp, HGVSp_Shor
 The acceptable values are HGVSp_Short, HGVSp, HGVSg and Genomic_Change(case-insensitive). Please see data/example.sh for examples.  
 If you do not specify query type, the MafAnnotator will try to figure out the query type based on the headers.  
 
-For HGVSp_Short, the annotator takes alteration from the column HGVSp_Short or Alteration  
-For HGVSp, the annotator takes alteration from the column HGVSp or Alteration  
-For HGVSg, the annotator takes alteration from the column HGVSg or Alteration  
-For Genomic_Change, the annotator takes genomic change from columns Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele1 and Tumor_Seq_Allele2.
+#### For HGVSp_Short
+The annotator takes alteration from the column HGVSp_Short or Alteration  
+
+#### For HGVSp
+The annotator takes alteration from the column HGVSp or Alteration  
+
+#### For HGVSg
+The annotator takes alteration from the column HGVSg or Alteration  
+
+#### For Genomic_Change
+The annotator takes genomic change from columns Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele1(Optional) and Tumor_Seq_Allele2.  
+Typically Tumor_Seq_Allele1 is the reference allele, Tumor_Seq_Allele2 is the variant allele. This is why Tumor_Seq_Allele1 is optional.  
+The annotator uses both if the value is different from Reference_Allele. Tumor_Seq_Allele2 has higher priority than Tumor_Seq_Allele1.  
 
 Annotation with Genomic_Change is relatively slow. We need to annotate the variant first with GenomeNexus(https://www.genomenexus.org/) then get annotation one by one. There is a plan to improve this method. If you are annotating a lot of data, please prioritize using other query type if applicable.