Fix: TSS and TTS now is corrected and documented

sqanti3_qc.py

@@ -884,12 +884,33 @@ def calc_exon_overlap(query_exons, ref_exons):
         return sum(q_bases.values())
 
     def get_diff_tss_tts(trec, ref):
+        # Calculating differences between transcript start sites (TSS) and
+        # Trasncript termination site (TTS) of two transcripts
         if trec.strand == '+':
-            diff_tss = trec.txStart - ref.txStart
-            diff_tts = trec.txEnd - ref.txEnd
+            # In positive (+) strand transcripts:
+            # TSS is calculated as reference start - transcript start
+            # TTS is calculated as transcript end - reference end
+            # This way,  TSS < 0 means the transcript is shortened, and 
+            # TSS > 0 means that transcript is elongated. Similarly, a
+            # TTS < 0 means that transcript is shortened, and a TTS > 0
+            # means that the transcript is elongated
+            diff_tss = ref.txStart - trec.txStart
+            diff_tts = trec.txEnd  - ref.txEnd
         else:
+            # In negative (-) strand transcripts:
+            # The transcripts in negative strands are loaded with trans.start = end
+            # and trans.end = start, to assure that trans.end > trans.start 
+            # regardless of the transcript. TTS and TSS are calculated with
+            # the same formula, but taking the loading fact into account,
+            # The formulas are inverted
+            # TTS is ref start - transcript start
+            # TSS is transcript end - treference end
+            # Being consistent in that  TSS < 0 means the transcript is shortened, and 
+            # TSS > 0 means that transcript is elongated. Similarly, a
+            # TTS < 0 means that transcript is shortened, and a TTS > 0
+            # means that the transcript is elongated
             diff_tts = ref.txStart - trec.txStart
-            diff_tss = ref.txEnd - trec.txEnd
+            diff_tss = trec.txEnd  - ref.txEnd
         return diff_tss, diff_tts
 
 
@@ -899,7 +920,7 @@ def get_gene_diff_tss_tts(isoform_hit):
         nearest_start_diff, nearest_end_diff = float('inf'), float('inf')
         for ref_gene in isoform_hit.genes:
             for x in start_ends_by_gene[ref_gene]['begin']:
-                d = trec.txStart - x
+                d =  x - trec.txStart
                 if abs(d) < abs(nearest_start_diff):
                     nearest_start_diff = d
             for x in start_ends_by_gene[ref_gene]['end']:
@@ -911,8 +932,8 @@ def get_gene_diff_tss_tts(isoform_hit):
             isoform_hit.tss_gene_diff = nearest_start_diff if nearest_start_diff!=float('inf') else 'NA'
             isoform_hit.tts_gene_diff = nearest_end_diff if nearest_end_diff!=float('inf') else 'NA'
         else:
-            isoform_hit.tss_gene_diff = -nearest_end_diff if nearest_start_diff!=float('inf') else 'NA'
-            isoform_hit.tts_gene_diff = -nearest_start_diff if nearest_end_diff!=float('inf') else 'NA'
+            isoform_hit.tss_gene_diff = nearest_end_diff if nearest_start_diff!=float('inf') else 'NA'
+            isoform_hit.tts_gene_diff = nearest_start_diff if nearest_end_diff!=float('inf') else 'NA'
 
     def categorize_incomplete_matches(trec, ref):
         """