minor changes

Author: Jon Palmer

bin/funannotate-functional.py

@@ -27,8 +27,6 @@ def __init__(self,prog):
 parser.add_argument('-i','--input', help='Folder from funannotate predict.')
 parser.add_argument('--genbank', help='Annotated genome in GenBank format')
 parser.add_argument('--fasta', help='Genome in FASTA format')
-parser.add_argument('--proteins', help='Proteins in FASTA format')
-parser.add_argument('--transcripts', help='Transcripts in FASTA format')
 parser.add_argument('--gff', help='GFF3 annotation file')
 parser.add_argument('-o','--out', help='Basename of output files')
 parser.add_argument('--sbt', default='SBT', help='Basename of output files')
@@ -452,7 +450,6 @@ def parseEggNoggMapper(input, output, GeneDict):
             sys.exit(1)
         else:
             Scaffolds = args.fasta
-            Transcripts = args.transcripts
             GFF = args.gff
             Proteins = os.path.join(outputdir, 'annotate_misc', 'genome.proteins.fa')
             TBL = os.path.join(outputdir, 'annotate_misc', 'genome.tbl')

lib/library.py

@@ -964,7 +964,7 @@ def _sortDict(d):
                         Genes[Parent]['CDS'].append((start, end))
                         Genes[Parent]['phase'].append(phase)
     if len(orphans) > 0:
-        log.error("GFF file is not properly sorted, i.e. gene, mRNA, exon, CDS")
+        log.error("GFF file parsing error, child features found without valid Parent. Check child/parent naming scheme.")
         sys.exit(1)
     #now sort dictionary by contig and location
     sGenes = sorted(Genes.iteritems(), key=_sortDict)