[META] SPECIES.PRODUCTION_NAME = Papilio_xuthus_pxut1 SPECIES.SCIENTIFIC_NAME = Papilio xuthus SPECIES.COMMON_NAME = Asian swallowtail SPECIES.DISPLAY_NAME = Papilio xuthus Pxut_1.0 SPECIES.DIVISION = EnsemblMetazoa SPECIES.URL = Papilio_xuthus_pxut1 SPECIES.TAXONOMY_ID = 66420 SPECIES.ALIAS = [ Papilio_xuthus_pxut1 papilio_xuthus_pxut1 Papilio%20xuthus%20Pxut_1.0 Papilio_xuthus_Pxut_1.0 Papilio_xuthus papilio_xuthus papilio_xuthus_pxut1 papilio%20xuthus Papilio%20xuthus asian%20swallowtail ] ASSEMBLY.NAME = Pxut_1.0 ASSEMBLY.DATE = 2015-02-02 ASSEMBLY.ACCESSION = GCA_000836235.1 ASSEMBLY.DEFAULT = Pxut_1.0 PROVIDER.NAME = Tokyo Institute of Technology PROVIDER.URL = http://papilio.nig.ac.jp/ GENEBUILD.ID = 2 GENEBUILD.START_DATE = 2016-08 GENEBUILD.VERSION = 2 GENEBUILD.METHOD = import [FILES] SCAFFOLD = [ fa http://papilio.bio.titech.ac.jp/genome-browser//download/px/scaffold.fasta.gz ] GFF = [ gff3 http://papilio.bio.titech.ac.jp/genome-browser//download/px/Pxuthus.v1.0.0.gff3.gz ] ; PROTEIN = [ fa http://papilio.bio.titech.ac.jp/genome-browser//download/px/Pxuthus.v1.0.0.pep.faa.gz ] ; perl -pe 's/>.+?\|/>/;' Pxuthus.v1.0.0.pep.faa > Pxuthus.v1.0.0.pep.renamed.faa PROTEIN = [ fa Pxuthus.v1.0.0.pep.renamed.faa ] [GFF] SORT = 1 ; SPLIT = [ ##FASTA GFF CONTIG ] CHUNK = [ change region ] CONDITION1 = [ MULTILINE CDS ] CONDITION1a = [ MULTILINE five_prime_utr ] CONDITION1b = [ MULTILINE three_prime_utr ] CONDITION1c = [ OVERRIDE CDS ID ] CONDITION1d = [ LACKS_ID cds make ] 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 /(.+)/ ] [EXTERNAL_DBS] [CODON_TABLE] MITOCHONDRION = [ mitochondrion ] [MODIFY] OVERWRITE_DB = 1 TRUNCATE_SEQUENCE_TABLES = 1 TRUNCATE_GENE_TABLES = 1 INVERT_PHASE = 1