fix newick tree visualization error when GCF == 2 bgcs

See merge request medema-group/BiG-SCAPE!31

- Fixed incompatibility of recursive glob in Python 2
- Added parameter --label. Will be used in the network_file folder +
visualization dropdown run names
- Removed annoying warning message from last time we broke backwards
compatibility. You are always advised to re-run everything from scratch
while BiG-SCAPE is in pre-release development! But we'll announce loss
of backward compatibility here

mibig bgcs are highlighted in the network

See merge request !30

Implemented loading screen (with html5 defer attribute)

See merge request !29

Fix bug when there is only 1 BGC in a class

See merge request !28

- hybrids mode is now default. Use --hybrids-off to turn it off
- cutoffs now has a single default value: 0.3
- clans clustering is now activated by default. Use --clans-off to turn
it off
- clan_cutoff is now 0.3 0.7 (i.e. will use GCFs defined at 0.3 and will
form GCC using average distance between GCFs of 0.7 or less)

Fixes issue #5. Some BGCs in MIBiG that don't have any domains were not
being removed from the mibig_set

- Query BGC mode. Bugfix. Was not using class-specific weights
- Query BGC mode. Small performance improvement; now prunes all non-relevant
distances
- MIBiG mode. Improvement: Now deletes all non-relevant MIBiG BGCs (uses
max(cutoffs) as reference)

Update & bugfix heatmap visualization

See merge request medema-group/BiG-SCAPE!27

Fix bug where GCF window stopped working

See merge request medema-group/BiG-SCAPE!26

Updated heatmap visualization

See merge request medema-group/BiG-SCAPE!25

Update heatmap visualization (todo: filter heatmap rows and columns to the top x…

See merge request medema-group/BiG-SCAPE!24

Update heatmap visualization (todo: filter heatmap rows and columns to the top x most significant members)

Use a designated BGC with --query_bgc (not necessarily in your
--inputdir) and search only for similar (up to max(cutoffs)) BGCs in
your data set.
- TODO: after the first round of QBGC vs all, delete distance
information from all non-relevant distances

- bigscape_results.js from the html template files was overwriting the
generated version with information about previous runs

Fix comparative view applying random offsets

See merge request medema-group/BiG-SCAPE!23

Implements Overview screen & related families view

See merge request medema-group/BiG-SCAPE!22

- Use original 'product' annotation from the original file if available
(hovering with mouse should present information, just as with domain
descriptions). Previously, only Gene name was used.

An internal array was limited to holding 1-byte unsigned numbers. This
effectively meant that your inpufiles could not contain more than 266
orfs

- Added another criteria to start glocal expansion: the seed slice
contains a core gene
- Don't include bgcs with unwanted classes very eary on (so don't
calculate domains, align them, keep their distances...)
- If CDSs overlap, allow for an overlap of up to 10% of the shortest CDS
(was causing trouble with some true positive overlapping CDSs)

- Use --mibig to automatically include the bundled BGCs from the MIBiG
database (it will decompress the files first)
- Note that at this point, many of the MIBiG's BGCs might not be
relevant to your analysis