Ptv 1637 fix

[jkbaumohl]

Genomes with empty contig_lists would create empty GFF files. This fixes that.

[lgtm-com[bot]]

This pull request introduces 1 alert when merging dbbf573259c4d9806dc6aee0d3316a89c33caab3 into f78c7e75dd11196555bce637fbf1841369ce068b - view on LGTM.com

new alerts:

• 1 for Variable defined multiple times

[jayrbolton]

Can you add a test for this?

[codecov[bot]]

Codecov Report

Merging #194 (2a87bb0) into master (f78c7e7) will increase coverage by 0.00%. The diff coverage is 80.00%.

@@           Coverage Diff           @@
##           master     #194   +/-   ##
=======================================
  Coverage   74.41%   74.41%           
=======================================
  Files          11       11           
  Lines        2873     2877    +4     
=======================================
+ Hits         2138     2141    +3     
- Misses        735      736    +1     

Impacted Files	Coverage Δ
lib/GenomeFileUtil/core/GenomeToGFF.py	76.36% <80.00%> (-0.04%)	:arrow_down:

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[jkbaumohl]

Can you add a test for this?

So this is a bit of an odd case in which 1 version of RAST created this odd scenario of the empty list for contig_ids. Additionally this is the first part I am going to change the save genome as well to insure that information is filled out properly, so I will not be able to save the gnome in the test once that is done. The fix is to address existing poorly formed genomes that the RAST code (and perhaps other have allowed). So honestly I am not even sure how to save a genome with this case after I put the other fix in place.

[jkbaumohl]

Can you add a test for this?

So this is a bit of an odd case in which 1 version of RAST created this odd scenario of the empty list for contig_ids. Additionally this is the first part I am going to change the save genome as well to insure that information is filled out properly, so I will not be able to save the gnome in the test once that is done. The fix is to address existing poorly formed genomes that the RAST code (and perhaps other have allowed). So honestly I am not even sure how to save a genome with this case after I put the other fix in place.