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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:
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 withroary input_data/*.gff -v
) fixes an input GFF file, the produced output infixed_input_files
looks like this:With the
##FASTA
directive, it looks like this:The text was updated successfully, but these errors were encountered: