Bug when output file already exists

[jhayer]

If the output file exists, the program should not write in the existing one but maybe overwrite. I got this error:

INFO:iss.generator:Cleaning up
Traceback (most recent call last):
File "/usr/local/bin/iss", line 11, in
sys.exit(main())
File "/usr/local/lib/python3.6/site-packages/iss/app.py", line 365, in main
args.func(args)
File "/usr/local/lib/python3.6/site-packages/iss/app.py", line 152, in generate_reads
generator.cleanup(temp_file_list)
File "/usr/local/lib/python3.6/site-packages/iss/generator.py", line 197, in cleanup
os.remove(temp_file + '_R1.fastq')
FileNotFoundError: [Errno 2] No such file or directory: '.iss.tmp.NC_010175.1.0_R1.fastq’

[HadrienG]

The problem was two fold:

• the --ncbi option was appending to already existing files. In the next release InSilicoSeq will exit if the output faster file exists
• In case they were duplicated ids in the input fast file, the reads were written to the same temporary file but were two separate entries in the cleanup function. The first remove worked fine but then the function failed when trying to remove the temporary file a second time.

Thanks for finding this bug!