No longer modify input contig file when fixing headers

src/fixContigHeaders.py

@@ -19,9 +19,9 @@ def fix_headers(fasta_in, fasta_out):
                         f2.write(f">{fixed_id}\n")
                         print(f'Header substitution: {original_id} replaced by {fixed_id}')
                     else:
-                        f2.write(line)
+                        f2.write(line.strip() + "\n")
                 else:
-                    f2.write(line)
+                    f2.write(line.strip() + "\n")
 
 if __name__ == "__main__":
     fix_headers(sys.argv[1], sys.argv[2])

src/mitohifi.py

@@ -182,8 +182,9 @@ def main():
         original_contigs = args.c
         fixContigHeaders.fix_headers(original_contigs, "fixed_header_contigs.fasta")
 
-        os.remove(original_contigs) # remove original contig file  
-        shutil.move("fixed_header_contigs.fasta", original_contigs) # replace original contigs file by the version that has the headers fixed
+        original_contigs = "fixed_header_contigs.fasta"
+        #os.remove(original_contigs) # remove original contig file  
+        #shutil.move("fixed_header_contigs.fasta", original_contigs) # replace original contigs file by the version that has the headers fixed
 
         # if contigs contain canu description of circularization, include that into the identifier
         modify_circularity_in_header(original_contigs, "include_circ_to_contigs_IDs.contigs.fasta")

src/modify_circularity_in_header.py

@@ -14,4 +14,4 @@ def modify_circularity_in_header(input_file, output_file):
                     new_header = f">{header}"
                 output_fasta.write(new_header + "\n")
             else:
-                output_fasta.write(line + "\n")
+                output_fasta.write(line.strip() + "\n")