Splitting algorithm

[joshfactorial]

Takes as input a fasta file with one or more contigs, and configuration file for a NEAT run. Has several command line options to specify output results.

Outputs, in a designated folder, several fasta files, and a corresponding NEAT read-simulator run configuration file for each, in which all the run parameters should be unchanged, and only the name set to correspond to the name of the file updated. These will suitable for a NEAT read-simulator run.

NOTES:

• Command line option for output location
• Command line option for breaking apart by size or by contig
  • If by contig, simply outputting the fasta split into contigs, with a configuration file each, is sufficient
  • If by file size, contig sequence should be split into files of approximately the size designated ( ~1mb, perhaps?). The sequences in consecutive files will overlap by approximately 2 read lengths to help patch the gaps between files.
  • Should be a check of disk space to prevent Python from crashing out if the OS runs out of space.
• Should be repeatable/deterministic for a given input, size, etc.