Merge pull request #18 from dev/right_normalize_variant

Right normalize variant

pyhgvs/tests/data/test_variants.genome

@@ -6,3 +6,9 @@ chr17	41246218	41246248	TTTACATATTAAAGCCTCATGAGGATCACT
 chr17	41246248	41246278	GGCCAGTAAGTCTATTTTCTCTGAAGAACC
 chr1	0	41	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 chr1	1	31	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+chr17	78078913	78078958	AACCGCCTCCACTTCACGGTGGGCAGGGCAGGGGCGGGGGCGGCG
+chr17	78078916	78078946	CGCCTCCACTTCACGGTGGGCAGGGCAGGG
+chr17	78078946	78078976	GCGGGGGCGGCGGCCAGGGCAGAGGGTGCG
+chr7	117199624	117199667	CACCATTAAAGAAAATATCATCTTTGGTGTTTCCTATGATGAA
+chr7	117199615	117199645	TATGCCTGGCACCATTAAAGAAAATATCAT
+chr7	117199648	117199678	TGGTGTTTCCTATGATGAATATAGATACAG

pyhgvs/tests/test_variants.py

@@ -17,31 +17,48 @@
 _normalize_tests = [
     # Simple SNP.
     (('chr17', 41246250, 'G', ['C']),
-     ('chr17', 41246250, 'G', ['C'])),
+     ('chr17', 41246250, 'G', ['C']),
+     'left'),
 
     # Left-align and 1bp pad.
     (('chr17', 41246251, '', ['G']),
-     ('chr17', 41246248, 'T', ['TG'])),
+     ('chr17', 41246248, 'T', ['TG']),
+     'left'),
 
     # Trim common prefix, left-align, and 1bp pad.
     (('chr17', 41246250, 'G', ['GG']),
-     ('chr17', 41246248, 'T', ['TG'])),
+     ('chr17', 41246248, 'T', ['TG']),
+     'left'),
 
     # Trim common prefix.
     (('chr17', 41246248, 'TGGC', ['TGGA']),
-     ('chr17', 41246251, 'C', ['A'])),
+     ('chr17', 41246251, 'C', ['A']),
+     'left'),
 
     # Trim common prefix and suffix.
     (('chr17', 41246248, 'TGGC', ['TGAC']),
-     ('chr17', 41246250, 'G', ['A'])),
+     ('chr17', 41246250, 'G', ['A']),
+     'left'),
 
     # Trim common prefix, triallelic
     (('chr17', 41246248, 'TGGC', ['TGGA', 'TGAC']),
-     ('chr17', 41246249, 'GGC', ['GAC', 'GGA'])),
+     ('chr17', 41246249, 'GGC', ['GAC', 'GGA']),
+     'left'),
 
     # Left edge of chromosome left justify, right pad.
     (('chr1', 5, 'NN', ['N']),
-     ('chr1', 1, 'NN', ['N'])),
+     ('chr1', 1, 'NN', ['N']),
+     'left'),
+
+    # Insertion. Trim common prefix, right-align, and 1bp pad.
+    (('chr17', 78078933, 'T', ['TGGGCA']),
+     ('chr17', 78078946, 'G', ['GCAGGG']),
+     'right'),
+
+    # Deletion. Trim common prefix, right-align, and 1bp pad.
+    (('chr7', 117199644, 'ATCT', ['A']),
+     ('chr7', 117199645, 'TCTT', ['T']),
+     'right')
 ]
 
 
@@ -55,10 +72,10 @@ def test_normalize_variant(self):
             filename='pyhgvs/tests/data/test_variants.genome',
             create_data=False)
 
-        for variant, true_variant in _normalize_tests:
+        for variant, true_variant, justify in _normalize_tests:
             chrom, offset, ref, alts = variant
             norm_variant = normalize_variant(
-                chrom, offset, ref, alts, genome).variant
+                chrom, offset, ref, alts, genome, justify=justify).variant
             self.assertEqual(
                 norm_variant, true_variant,
                 'Variant failed to normalize %s: %s != %s' %

pyhgvs/variants.py

@@ -113,7 +113,7 @@ def justify_genomic_indel(genome, chrom, start, end, indel, justify,
 
 
 def normalize_variant(chrom, offset, ref_sequence, alt_sequences, genome,
-                      flank_length=30):
+                      justify='left', flank_length=30):
     """
     Normalize variant according to the GATK/VCF standard.
 
@@ -131,7 +131,7 @@ def normalize_variant(chrom, offset, ref_sequence, alt_sequences, genome,
         chrom_stop=end,
         is_forward_strand=True)
     return NormalizedVariant(position, ref_sequence, alt_sequences,
-                             genome=genome)
+                             genome=genome, justify=justify)
 
 
 class NormalizedVariant(object):
@@ -140,7 +140,7 @@ class NormalizedVariant(object):
     """
 
     def __init__(self, position, ref_allele, alt_alleles,
-                 seq_5p='', seq_3p='', genome=None):
+                 seq_5p='', seq_3p='', genome=None, justify='left'):
         """
         position: a 0-index genomic Position.
         ref_allele: the reference allele sequence.
@@ -159,7 +159,7 @@ def __init__(self, position, ref_allele, alt_alleles,
         self._on_forward_strand()
         self._trim_common_prefix()
         self._trim_common_suffix()
-        self._left_align()
+        self._align(justify)
         self._1bp_pad()
         self._set_1based_position()
 
@@ -215,11 +215,11 @@ def _trim_common_suffix(self):
             for i, allele in enumerate(self.alleles):
                 self.alleles[i] = allele[:-common_suffix]
 
-    def _left_align(self):
+    def _align(self, justify):
         """
-        Align variant as far to the left as possible.
+        Align variant as far to the left or right as possible.
         """
-        # Left-aligning only makes sense for INDELs.
+        # Aligning only makes sense for INDELs.
         if self.molecular_class != "INDEL":
             return
 
@@ -236,7 +236,11 @@ def _left_align(self):
                 start, end, allele = justify_genomic_indel(
                     self.genome, self.position.chrom,
                     self.position.chrom_start, self.position.chrom_stop,
-                    allele, 'left')
+                    allele, justify)
+                # if right-aligning an insertion, insert at the end
+                if justify == 'right' and i != 0:
+                    start += len(allele)
+                    end += len(allele)
                 self.position.chrom_start = start
                 self.position.chrom_stop = end
                 flank_length = 30
@@ -248,7 +252,7 @@ def _left_align(self):
             else:
                 offset = len(self.seq_5p)
                 offset2, _, allele = justify_indel(
-                    offset, offset, allele, self.seq_5p, 'left')
+                    offset, offset, allele, self.seq_5p, justify)
                 delta = offset - offset2
                 if delta > 0:
                     self.position.chrom_start -= delta

setup.py

@@ -20,7 +20,7 @@ def main():
 
     setup(
         name='pyhgvs',
-        version='0.9.4',
+        version='0.9.5',
         description='HGVS name parsing and formatting',
         long_description=description,
         author='Matt Rasmussen',