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Refactoring code and fixing cutoff argument handling #4

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Refactoring code and fixing cutoff argument handling #4

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This commit contains the following changes:

  1. Correct behaviour and help string for --cutoff argument. I set the default value to 0.02. Consider changing it back to 0 if it is a problem.
  2. Refactoring code: dividing into separate functions for better readability.

@serzero2007
Move generating input for fasta35 into a separate function
2f77c56
@serzero2007
Fix --cutoff flag type and help message
5daabb8 
According to the source code the cutoff flag is minimum protein
importance value for it to be included into selected_proteins list.
The previous flag definition was misleading and had incorrect type,
making the flag unusable, because any non-zero integer cutoff value
would result in no protein selected at all.
@serzero2007
Remove unused fasta35 function
101f05e
@serzero2007
Move parsing arguments logic into its own function
656ac6f
@serzero2007
Remove redundant import
3c55db6
@serzero2007
Move code for running fasta35 into spawn_fasta35
7f2d772
@serzero2007
define select_genomes, select_proteins functions
680c229
@serzero2007
Define train_random_forest function
db80f8e
@serzero2007
Define parse_fasta35_scores function
8d4dccb
@serzero2007
Use len(...) instead of value from args
e72b642
@serzero2007
No fail if len(selected_proteins) < num_proteins
d18f515
@serzero2007
No fail if len(labels[label]) < args.num_genomes
d29d12b
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@serzero2007