[META] SPECIES.PRODUCTION_NAME = Papilio_xuthus_papxu1 SPECIES.SCIENTIFIC_NAME = Papilio xuthus SPECIES.COMMON_NAME = Asian swallowtail SPECIES.DISPLAY_NAME = Papilio xuthus Pap_xu_1.0 SPECIES.DIVISION = EnsemblMetazoa SPECIES.URL = Papilio_xuthus_papxu1 SPECIES.TAXONOMY_ID = 66420 SPECIES.ALIAS = [ Papilio_xuthus_papxu1 papilio_xuthus_papxu1 Papilio%20xuthus%20Pap_xu_1.0 Papilio_xuthus_Pap_xu_1.0 Papilio_xuthus papilio_xuthus papilio_xuthus_papxu1 papilio%20xuthus Papilio%20xuthus asian%20swallowtail ] ASSEMBLY.NAME = Pap_xu_1.0 ASSEMBLY.DATE = 2015-09-28 ASSEMBLY.ACCESSION = GCA_001298345.1 ASSEMBLY.DEFAULT = Pap_xu_1.0 PROVIDER.NAME = BGI PROVIDER.URL = GENEBUILD.ID = 2 GENEBUILD.START_DATE = 2016-08 GENEBUILD.VERSION = 2 GENEBUILD.METHOD = import [GFF] SORT = 1 ; SPLIT = [ ##FASTA GFF CONTIG ] CHUNK = [ change region ] ; CHUNK = [ separator ### ] CONDITION1 = [ MULTILINE CDS ] CONDITION1a = [ MULTILINE cDNA_match ] CONDITION1b = [ MULTILINE match ] 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 force ]; CONDITION7 = [ EXPECTATION ncrna hasParent gene force ]; CONDITION8 = [ EXPECTATION trna hasParent gene force ]; CONDITION9 = [ EXPECTATION transcript hasParent gene force ]; CONDITION10 = [ EXPECTATION cds|exon|mrna|transcript|trna|ncrna|gene <=[_start,_end] SELF warn ]; [FILES] SCAFFOLD = [ fa ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001298345.1_Pap_xu_1.0/GCA_001298345.1_Pap_xu_1.0_genomic.fna.gz ] ;curl ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001298345.1_Pap_xu_1.0/GCA_001298345.1_Pap_xu_1.0_genomic.gff.gz \ ;| zcat | perl -lne ' ;BEGIN{ ; %cds = qw(KPJ01109.1 1 KPJ01246.1 1 KPJ20781.1 1 KPJ20788.1 1 KPJ20792.1 1 KPJ20811.1 1) ;}{ ; @F=split/\t/; ; if ($F[2] eq "CDS" and $F[8] =~/Name=([^;]+)/ and defined $cds{$1}) { ; $F[7] = (3 - $F[7]) % 3; ; } ; print join("\t",@F) ;}' >GCA_001298345.1_Pap_xu_1.0_genomic.corr6cds.gff ; GFF = [ gff3 http://download.lepbase.org/v3/provider/GCA_001298345.1_Pap_xu_1.0_genomic.corr6cds.gff.gz ] GFF = [ gff3 http://download.lepbase.org/v3/annotation/Papilio_xuthus_Pap_xu_1.0_-_genes.gff.gz ] SCAFFOLD_NAMES = [ tsv ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001298345.1_Pap_xu_1.0/GCA_001298345.1_Pap_xu_1.0_assembly_structure/Primary_Assembly/scaffold_localID2acc ] PROTEIN = [ fa ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001298345.1_Pap_xu_1.0/GCA_001298345.1_Pap_xu_1.0_protein.faa.gz ] [GENE_STABLE_IDS] GFF = [ gene->Name /(.+)/ ] [GENE_DESCRIPTIONS] GFF = [ 1 mRNA->product /(.+)/ ] [GENE_NAMES] ; GFF = [ 1 SELF->Name /(.+)/ ] [TRANSCRIPT_DESCRIPTIONS] GFF = [ 1 SELF->product /(.+)/ ] [TRANSCRIPT_STABLE_IDS] GFF = [ CDS->Name /(.+)/ ] [TRANSCRIPT_NAMES] ; GFF = [ SELF->transcript_id /(.+)/ ] [TRANSLATION_STABLE_IDS] GFF = [ SELF->Name /(.+)/ ] [DBXREFS] ; Pattern matching to associate Dxref attributes in the GFF with the correct database ; KEY = [ EXTERNAL_DB_ID NAME ACCESSION_REGEX DISPLAY_NAME_REGEX ] GO = [ 1000 GO /^goslim_goa:GO:(.+)/ ] INTERNAL = [ 9999 Internal /^Internal:(.+)/ /^Internal:(.+)/ ] REFSEQ_MRNA = [ 1801 RefSeq_mRNA /^Genbank:(NM_.+)/ ] REFSEQ_MRNA_PRED = [ 1806 RefSeq_mRNA_predicted /^Genbank:(XM_.+)/ ] REFSEQ_PEPTIDE = [ 1810 RefSeq_peptide /^Genbank:(NP_.+)/ ] REFSEQ_PEPTIDE_PRED = [ 1815 RefSeq_peptide_predicted /^Genbank:(XP_.+)/ ] REFSEQ_RNA = [ 1820 RefSeq_rna /^Genbank:(XR_.+)/ ] REFSEQ_RNA_PRED = [ 1825 RefSeq_rna_predicted /^Genbank:(XR_.+)/ ] ENTREZGENE = [ 1300 EntrezGene /^GeneID:(.+)/ ] INTERPROSCAN = [ 1200 InterProScan /^InterPro:(.+)/ ] UNIPROT = [ 2250 UniProtKB /^UniProtKB\/Swiss-Prot:(.+)/ ] GENBANK = [ 50688 GenBank /^NCBI_GP:(.+)/ ] [EXTERNAL_DBS] [MODIFY] OVERWRITE_DB = 1 TRUNCATE_SEQUENCE_TABLES = 1 TRUNCATE_GENE_TABLES = 1 [SCAFFOLD_NAMES] HEADER = 1 ; Define patterns for producing contig and scaffold synonyms SCAFFOLD = [ /(.+)/ ] CONTIG = [ /(.+)/ ]