[META] SPECIES.PRODUCTION_NAME = Heliconius_erato_lativitta_v1 SPECIES.SCIENTIFIC_NAME = Heliconius erato lativitta SPECIES.COMMON_NAME = Crimson-patched longwing SPECIES.DISPLAY_NAME = Heliconius erato lativitta v1 SPECIES.DIVISION = EnsemblMetazoa SPECIES.URL = Heliconius_erato_lativitta_v1 SPECIES.TAXONOMY_ID = 1608923 SPECIES.ALIAS = [ Heliconius%20erato%20lativitta lativitta erato Heliconius_erato longwing ] ASSEMBLY.NAME = v1 ASSEMBLY.DATE = 2016-09-12 ASSEMBLY.ACCESSION = ASSEMBLY.DEFAULT = v1 PROVIDER.NAME = Reed Lab PROVIDER.URL = http://www.reedlab.org/ GENEBUILD.ID = 1 GENEBUILD.START_DATE = 2016-10 GENEBUILD.VERSION = 1 GENEBUILD.METHOD = import [GFF] SORT = 0 ; SPLIT = [ ##FASTA GFF CONTIG ] CHUNK = [ change region ] ; CHUNK = [ separator ### ] CONDITION1 = [ MULTILINE CDS ] CONDITION1c = [ MULTILINE five_prime_utr ] CONDITION1d = [ MULTILINE three_prime_utr ] ; CONDITION1e = [ OVERRIDE CDS ID ] ; CONDITION1f = [ LACKS_ID cds make ] ; CONDITION2 = [ EXPECTATION cds hasSister exon force ] ; CONDITION3 = [ EXPECTATION cds hasParent mrna force ]; ; CONDITION4 = [ EXPECTATION exon hasParent transcript|mrna|trna|ncrna force ]; ; CONDITION5 = [ EXPECTATION mrna hasParent gene warn ]; ; CONDITION7 = [ EXPECTATION ncrna hasParent gene warn ]; ; CONDITION8 = [ EXPECTATION trna hasParent gene warn ]; ; CONDITION9 = [ EXPECTATION transcript hasParent gene warn ]; ; CONDITION10 = [ EXPECTATION cds|exon|mrna|transcript|trna|ncrna|gene <=[_start,_end] SELF warn ]; [FILES] SCAFFOLD = [ fa http://download.lepbase.org/v4/provider/Hel_final_2016.fa.gz ] ; curl http://download.lepbase.org/v4/provider/hel_2016_v3.all.renamed.gff.gz | zgrep -P "\tmaker\t" | perl -lne 'print "###" if /\tgene\t/;s/;LengtHel_chr17_6/;\nHel_chr17_6/;print' >hel_2016_v3.all.renamed.maker.gff GFF = [ gff3 hel_2016_v3.all.renamed.maker.gff ] PROTEIN = [ fa http://download.lepbase.org/v4/provider/hel_2016_v3.all.maker.proteins.renamed.fasta.gz ] [GENE_DESCRIPTIONS] [GENE_STABLE_IDS] GFF = [ gene->ID /(.+)/ ] [GENE_NAMES] [TRANSCRIPT_DESCRIPTIONS] [TRANSCRIPT_STABLE_IDS] GFF = [ SELF->ID /(.+)/ ] [TRANSCRIPT_NAMES] [TRANSLATION_STABLE_IDS] GFF = [ mRNA->ID /(.+)/ ] [MODIFY] OVERWRITE_DB = 1 TRUNCATE_SEQUENCE_TABLES = 1 TRUNCATE_GENE_TABLES = 1 INVERT_PHASE = 0 [EXTERNAL_DBS]