GFF parsing doesn't match GFF3 specification

[widdowquinn]

For correct operation, the Roary GFF parser appears to require the ##FASTA directive to indicate a trailing FASTA sequence for the input genome, but the GFF3 specification ("Other Syntax") allows this to be implicit:

"For backward-compatibility with the GFF version output by the Artemis tool, a GFF line that begins with the character > creates an implied ##FASTA directive."

Without the ##FASTA directive, when Roary (invoked with roary input_data/*.gff -v) fixes an input GFF file, the produced output in fixed_input_files looks like this:

[...]
NZ_CM001513.1   RefSeq  gene    6178796 6179191 .   +   .   ID=gene5445___11243;Name=PFLSS101_RS27240;gbkey=Gene;gene_biotype=pseudogene;locus_tag=PFLSS101_RS27240;pseudo=true
NZ_CM001513.1   Protein Homology    CDS 6178796 6179191 .   +   0   ID=cds5355___11244;Parent=gene5445;gbkey=CDS;product=hypothetical protein;pseudo=true;transl_except=(pos:6179072..6179074%2Caa:Other);transl_table=11
###
>NZ_CM001513.1 Pseudomonas fluorescens SS101 chromosome, whole genome shotgun sequence
                                ID=id___11245CAGAGAATGACAACACGGGGGAGAAGCGGTGCTCTGCCTGTGCTGCGCTATCGGATAAGCTGTGTGTGGAACAGCTAGTT
                                ID=id___11246ATCCACAGGTCGGTTACCCACAGACTTTCGACCCCACTTGTACAATGAGCTTAGGTGGGTTTATCCACAGAGCTTATGCA
                                ID=id___11247CAGACCACTGGTCGCATTTTTTAGGGTTAAGGCATTGATTTTGGGTGTCCTGTGAGCAACCTACATGTGGATAAGTGGAC
[...]

With the ##FASTA directive, it looks like this:

NZ_CP010945.1   tRNAscan-SE exon    6997911 6997987 .   -   .   ID=id190___24142;Parent=rna90;anticodon=(pos:complement(6997951..6997953));gbkey=tRNA;product=tRNA-Ile
NZ_CP010945.1   RefSeq  sequence_feature    6998060 6998154 .   -   .   ID=id191___24143;Note=16S ribosomal RNA rRNA prediction is too short;gbkey=misc_feature
##FASTA
>NZ_CP010945.1 Pseudomonas fluorescens NCIMB 11764, complete genome
TTACCGGGGCTTCGATCAAGAGCTTCGCGTTAGCTAACCCCATCAATTAACCTTCCGGCACCGGGCAGGCGTCACACCCT
ATACGTCCACTTTCGTGTTTGCAGAGTGCTGTGTTTTTAATAAACAGTCGCAGCGGCCTGGTATCTTCGACCGGCATGAG
CTTACGGAGCAAGTCCTTCACCCTCACCGGCGCACCTTCTCCCGAAGTTACGGTGCCATTTTGCCTAGTTCCTTCACCCG
AGTTCTCTCAAGCGCCTTGGTATTCTCTACCCAACCACCTGTGTCGGTTTGGGGTACGGTTCCTGGTTACCTGAAGCTTA