Fix off by one error and lowercase cds

tools/process_spaln_output.py

@@ -32,7 +32,7 @@ def fix(attrs, region_name, number):
 
 output_filename = "spaln_out.gff3"
 output_file = open(output_filename, "w")
-print('##gff-version\t3', file=output_file)
+print("##gff-version\t3", file=output_file)
 input_filenames = sys.argv[1:]
 seen_header = False
 gene_number = 0
@@ -42,7 +42,7 @@ def fix(attrs, region_name, number):
 max_end = 0
 for input_filename in input_filenames:
     for line in open(input_filename):
-        if line.startswith('##sequence-region'):
+        if line.startswith("##sequence-region"):
             parts = line.split()
             orig_region_name = parts[1]
             location_parts = parts[1].split(":")
@@ -51,10 +51,10 @@ def fix(attrs, region_name, number):
             if region_name not in annotation_parts:
                 annotation_parts[region_name] = []
             annotation_parts[region_name].append((start, region_name, input_filename))
-        elif not line.startswith('#'):
+        elif not line.startswith("#"):
             fields = line.rstrip().split("\t")
             seq_type = fields[2]
-            if seq_type == 'gene':
+            if seq_type == "gene":
                 # end is fields[4]
                 max_end = int(fields[4]) + start
     else:
@@ -68,26 +68,39 @@ def fix(attrs, region_name, number):
     sequence_region_added = False
     for start, region_name, input_filename in sorted(locations, key=itemgetter(0)):
         if not sequence_region_added:
-            assert start == start_position[region_name], "mismatch between this start position {} and computed start position {} for {}".format(start, start_position[region_name], region_name)
+            assert (
+                start == start_position[region_name]
+            ), "mismatch between this start position {} and computed start position {} for {}".format(
+                start, start_position[region_name], region_name
+            )
             # started a new contig, add a sequence region header that describes the region under annotation
-            print('##sequence-region\t{} {} {}'.format(region_name, start, end_position[region_name]), file=output_file)
+            print(
+                "##sequence-region\t{} {} {}".format(
+                    region_name, start, end_position[region_name]
+                ),
+                file=output_file,
+            )
             sequence_region_added = True
 
         for line in open(input_filename):
-            if line.startswith("##sequence-region") or line.startswith('##gff-version'):
+            if line.startswith("##sequence-region") or line.startswith("##gff-version"):
                 continue
-            elif line.startswith('##FASTA'):
+            elif line.startswith("##FASTA"):
                 break
-            elif line.startswith('##'):
-                print('Warning: unexpected directive {}'.format(line.strip()), file=output_file)
+            elif line.startswith("##"):
+                print(
+                    "Warning: unexpected directive {}".format(line.strip()),
+                    file=output_file,
+                )
                 continue
             fields = line.rstrip().split("\t")
             seq_type = fields[2]
             if seq_type == "gene":
                 gene_number += 1
             fields[0] = region_name
-            fields[3] = str(int(fields[3]) + start)
-            fields[4] = str(int(fields[4]) + start)
+            fields[2] = "CDS" if fields[2] == "cds" else fields[2]
+            fields[3] = str(int(fields[3]) + start - 1)
+            fields[4] = str(int(fields[4]) + start - 1)
             fields[8] = fix(fields[8], region_name, gene_number)
             new_line = "\t".join(fields)
             print(new_line, end="", file=output_file)