[META] SPECIES.PRODUCTION_NAME = Plodia_interpunctella_v1 SPECIES.SCIENTIFIC_NAME = Plodia interpunctella SPECIES.COMMON_NAME = Indian mealmoth SPECIES.DISPLAY_NAME = Plodia interpunctella v1 SPECIES.DIVISION = EnsemblMetazoa SPECIES.URL = Plodia_interpunctella_v1 SPECIES.TAXONOMY_ID = 58824 SPECIES.ALIAS = [ Plodia_interpunctella_v1 plodia_interpunctella_v1 plodia Plodia%20interpunctella%20v1 Plodia_interpunctella_v1 plodia_interpunctella_v1 plodia_interpunctella Plodia_interpunctella plodia%20interpunctella%20v1 plodia%20interpunctella Plodia%20interpunctella mealmoth Indian%20mealmoth ] ASSEMBLY.NAME = v1 ASSEMBLY.DATE = 2015-04-03 ASSEMBLY.ACCESSION = ASSEMBLY.DEFAULT = v1 PROVIDER.NAME = Steve Paterson Lab PROVIDER.URL = http://www.liv.ac.uk/genomic-research/ GENEBUILD.ID = 2 GENEBUILD.START_DATE = 2015-07 GENEBUILD.VERSION = 2016-08 GENEBUILD.METHOD = import [FILES] CONTIG = [ fa http://download.lepbase.org/v3/provider/PRJEB4871_formatted_for_agp.fa.gz ] SCAFFOLD = [ agp http://download.lepbase.org/v3/provider/PRJEB4871.agp.gz ] ; GFF = [ gff3 http://download.lepbase.org/v3/provider/plodiav1.rephased.genes.gff3.gz ] ; GFF = [ gff3 maker.gff3 ] GFF = [ gff3 http://download.lepbase.org/v3/annotation/Plodia_interpunctella_v1_-_genes.gff.gz ] SCAFFOLD_NAMES = [ tsv http://download.lepbase.org/v3/provider/plodiav1.synonyms.txt ] [GFF] SORT = 1 CHUNK = [ change region ] CONDITION1 = [ MULTILINE CDS ] CONDITION1a = [ MULTILINE five_prime_utr ] CONDITION1b = [ MULTILINE three_prime_utr ] CONDITION2 = [ EXPECTATION cds hasSister exon force ] CONDITION3 = [ EXPECTATION mrna hasParent gene force ]; CONDITION6 = [ EXPECTATION exon hasParent mrna force ]; CONDITION7 = [ EXPECTATION cds hasParent mrna force ]; CONDITION8 = [ EXPECTATION cds|exon|mrna|gene <=[_start,_end] SELF skip ]; [GENE_DESCRIPTIONS] GFF = [ 1 gene->description /(.+)/ ] [GENE_STABLE_IDS] GFF = [ gene->ID /(.+)/ ] [GENE_NAMES] [TRANSCRIPT_DESCRIPTIONS] [TRANSCRIPT_STABLE_IDS] GFF = [ SELF->ID /(.+)/ ] [TRANSCRIPT_NAMES] [TRANSLATION_STABLE_IDS] GFF = [ SELF->ID /(.+)/ ] [DBXREFS] [EXTERNAL_DBS] [MODIFY] OVERWRITE_DB = 1 TRUNCATE_SEQUENCE_TABLES = 1 TRUNCATE_GENE_TABLES = 1 [SCAFFOLD_NAMES] ; Define whether the SCAFFOLD_NAMES file has a header row HEADER = 0 ; Define patterns for producing contig and scaffold synonyms ; SCAFFOLD = [ /_(\d+)$/ /(\d+)/scaf$1/ ]