The program sometimes clears all contents of source sequence files

[heqin-zhu]

I find that the program sometimes will truncate source files, namely clear all contents of the source files. After checking the code, I find the following function that convert multi-line fasta to single-line fasta. Perhaps writing to a new file instead of origin source file will be better.

SPOT-RNA/SPOT-RNA.py

Line 25 in dfd0277

FastaMLtoSL(args.inputs)

SPOT-RNA/utils/FastaMLtoSL.py

Line 51 in dfd0277

with open(outFile,"w") as newFasta: