Replace extractcounts.py

scripts/extractcounts.py

@@ -32,10 +32,11 @@ def parse_gtf(in_file, read_length = 100):
                 # turn into into int to do calculations
                 trans_len = abs(int(line_cont[4])-int(line_cont[3]))
                 gene_info = line_cont[8].split(' ')
-                if len(gene_info) == 16:
-                    gene_name = gene_info[9].lstrip('"').rstrip('";')
-                    cov = float(gene_info[11].lstrip('"').rstrip('";'))
-                    genes[gene_name] = round(cov * trans_len /read_length)
+                if len(gene_info) == 12:
+                    gene_name = gene_info[5].lstrip('"').rstrip('";')
+                    cov = float(gene_info[7].lstrip('"').rstrip('";'))
+                    if cov > 0.01:
+                        genes[gene_name] = round(cov * trans_len /read_length)
         return genes