Fixed incorrect strand assignment for "-" RNAs and improved subject_d…

…ropped.bed to liftOver coordinates.

ortho2align/genomicranges.py

@@ -1210,7 +1210,7 @@ def _prepare_side(self, side='q'):
                            max(self.HSPs, key=lambda i: i.send).send)
             name = self.alignment.srange.name
             strand = nxor_strands(self.HSPs[0].sstrand,
-                                  self.alignment.srange.strand)
+                                  self.alignment.qrange.strand)
             blockSizes = [abs(hsp.send - hsp.sstart) for hsp in self.HSPs]
             blockPvals = [hsp.pval for hsp in self.HSPs]
             if strand == "+":
@@ -1850,6 +1850,20 @@ def to_bed6(self, fileobj):
                                      '.',
                                      str(grange.strand)]) + '\n')
 
+    def drop_duplicates(self):
+        if len(self) <= 1:
+            return self
+        new_ranges = list()
+        new_ranges.append(self[0])
+        for grange in self[1:]:
+            if grange == new_ranges[-1]:
+                continue
+            new_ranges.append(grange)
+        used_args = {'collection', }
+        kwargs = {attr: getattr(self, attr)
+                  for attr in set(self.init_args) - used_args}
+        return self.__class__(new_ranges, **kwargs)
+
 
 class GenomicRangesList(BaseGenomicRangesList):
     """Represents a list of `GenomicRange` instances.

ortho2align/pipeline.py

@@ -884,13 +884,30 @@ def build_orthologs(alignments,
                                    for group in subject_orthologs
                                    for ortholog in group
                                    if ortholog]
-        query_dropped = BaseGenomicRangesList([item[0]
-                                               for item in dropped_ranges
-                                               if item])
-        subject_dropped = BaseGenomicRangesList([srange
-                                                 for item in dropped_ranges
-                                                 if item
-                                                 for srange in item[1]])
+        query_dropped = list()
+        subject_dropped = list()
+        for item in dropped_ranges:
+            if len(item) != 2:
+                continue
+            query_dropped_range, subject_dropped_ranges = item
+            query_dropped.append(query_dropped_range)
+            print(query_dropped_range.name)
+            for grange in subject_dropped_ranges:
+                print(grange)
+                subject_lifts = grange.find_neighbours(query_dropped_range.relations['lifted'])
+                print(subject_lifts)
+                subject_dropped.append(subject_lifts)
+        query_dropped = BaseGenomicRangesList(query_dropped)
+        subject_dropped = BaseGenomicRangesList(srange
+                                                for group in subject_dropped
+                                                for srange in group).drop_duplicates()
+        # query_dropped = BaseGenomicRangesList([item[0]
+        #                                        for item in dropped_ranges
+        #                                        if item])
+        # subject_dropped = BaseGenomicRangesList([srange
+        #                                          for item in dropped_ranges
+        #                                          if item
+        #                                          for srange in item[1]])
         total_dropped = len(query_dropped)
         query_exception_list = BaseGenomicRangesList(query_exception_ranges)
 

setup.py

@@ -2,7 +2,7 @@
 
 
 setup(name='ortho2align',
-      version='1.0.1',
+      version='1.0.3',
       description='A lncRNA ortholog discovery tool based on syntenic regions and statistical assessment of alignment nonrandomness.',
       url='http://github.com/dmitrymyl/ortho2align',
       author='Dmitry Mylarshchikov',