Pyamilyseq

This is a major release that has undergone another large rewrite to reduce redundancy of code, fix a number of bugs and re-add back in the Genus mode.

- PyamilySeq now as default outputs a 'summary_statistics.txt' file in a similar output to what Panaroo and Roary does.


-group_mode {Species,Genus}
Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode?

Clustering Runtime Arguments - Optional when "-run_mode Full" is used:
-mem CLUSTERING_MEMORY
Default 4000: Memory to be allocated for clustering (in MBs).
-t CLUSTERING_THREADS
Default 4: Threads to be allocated for clustering.

Thanks to ecampbell50 for identifying a broken import here: https://github.com/NickJD/PyamilySeq/issues/1

Genus mode has been removed while it is still under development.
` -group_mode {Species}
Group Mode: Should PyamilySeq be run in "Species" or
"Genus" mode? - Genus mode not currently functioning`

This release marks the first 'fully working' version of PyamilySeq. There are likely still many bugs and missing features but the core is now stable.
The main change is the UI itself - PyamilySeq has been separated into two run modes - Either 'Full' or 'Partial'.
` -run_mode {Full,Partial}
Run Mode: Should PyamilySeq be run in "Full" or
"Partial" mode?`

This release also features 'Seq-Combiner' that can be used to extract and combine the CDS sequences from multiple GFF files ready for a user to perform external clustering (PyamilySeq can do the entire process itself by calling cd-hit if you user wants).

Seq-Combiner: `Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output_dir.../test_data -output_name combine_fasta_seqs.fa -input_type combined`

- A fair amount of internal reworking done
- PyamilySeq can now internally call mafft to align the individual gene groups and concatenate them ready for phylogenetic tree building.

` -con CON_CORE Default - No output: Output aligned and concatinated sequences of identified families - used for MSA (provide levels at which to
output "-w 99,95" - Must provide FASTA file with -fasta`

New user options added:

Output Parameters:
-w WRITE_FAMILIES Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95" - Must provide FASTA file with -fasta
-fasta FASTA FASTA file to use in conjunction with "-w"