;;========================================================================== ;; Sample genetic-elements.dat file. ;; ;; This file contains a set of records, one for each genetic element ;; (chromosome, plasmid, etc.) or contig in the organism. Each genetic ;; element can be described by either a single annotation file or a ;; set of annotation files, each associated with a single contig ;; belonging to the genetic element. Records are terminated by a ;; single line containing only the string "//". (The "//" is also ;; required after the final genetic element.) Each record contains a ;; set of attribute-value pairs, one per line, separated by the tab ;; character. Lines beginning with ; are comment lines. Valid ;; attributes are: ;; ;; ID ;; Required. Identifier for the genetic element. The identifer must ;; be unique with respect to all other identifiers used in the PGDB, ;; such as gene and protein identifiers. The ID should start with an ;; alphabetic character, and contain no spaces or special ;; characters. Numbers are allowed, as are dashes and underscores. ;; Case insensitive. ;; ;; NAME ;; Required. Descriptive name for the genetic element. ;; ;; TYPE ;; Optional. One of :CHRSM, :PLASMID, :CONTIG, :MT (mitochondrial ;; chromosome), or :PT (chloroplast chromosome). Defaults to :CHRSM. ;; ;; CIRCULAR? ;; Required (except for contigs). Is the genetic element circular? ;; One of Y or N. ;; ;; CODON-TABLE ;; Optional; defaults to the codon table specified in the ;; organism.dat file, or to the standard codon-table if not ;; supplied. This should be a number between 1 and 15. ;; ;; ANNOT-FILE ;; Required, unless the CONTIG attribute is supplied. Filename for ;; the annotation file for this genetic element. The file must be in ;; either PathoLogic format (file suffix .pf) or GenBank format ;; (file suffix .gb or .gbk). If a GenBank file is supplied, the ;; SEQ-FILE attribute (see below) should be omitted, and the ;; sequence of the genetic element will be extracted from this ;; file. If the file is in the cyc//input/ directory, ;; then only the filename is required, otherwise a full pathname ;; must be supplied. ;; ;; SEQ-FILE ;; Optional. Filename for the sequence file for this genetic ;; element. The file must be in FASTA format (file suffix .fna, ;; .fsa, .fa, .fasta, or .seq). If the ANNOT-FILE attribute ;; specifies a file in GenBank format, the SEQ-FILE attribute may be ;; omitted, and the genetic element sequence will be extracted from ;; the GenBank file. If the file is in the cyc//input/ ;; directory, then only the filename is required, otherwise a full ;; pathname must be supplied. ;; ;; CONTIG ;; Optional (but not permitted in records of type :CONTIG). ID for a ;; contig that forms part of this genetic element. A genetic element ;; may have multiple CONTIG lines. This field should not be supplied ;; if the ANNOT-FILE attribute is supplied. Syntax requirements same ;; as ID. ;;=========================================================================== ;; A chromosome with annotation provided in PathoLogic format. ID TEST-CHROM-1 NAME Chromosome 1 TYPE :CHRSM CIRCULAR? N ANNOT-FILE chrom1.pf SEQ-FILE chrom1.fsa // ;; A chromosome with annotation provided in GenBank format; SEQ-FILE ;; omitted (sequence will be extracted from the GenBank file). ID TEST-CHROM-2 NAME Chromosome 2 CIRCULAR? N ANNOT-FILE /mydata/chrom2.gbk // ;; A mitochondrial chromosome with no sequence data. ID TEST-MIT-CHROM NAME Mitochondrial chromosome TYPE :MT CIRCULAR? Y CODON-TABLE 2 ANNOT-FILE mit-chrom.pf // ;; A chromosome with two contigs, whose IDs are given by the CONTIG ;; attributes. ID TEST-CHROM-3 NAME Chromosome 3 TYPE :CHRSM CIRCULAR? N CONTIG CONTIG-1 CONTIG CONTIG-2 // ;; The two contig records associated with TEST-CHROM-3. ID CONTIG-1 NAME Contig 1 of Chromosome 3 TYPE :CONTIG ANNOT-FILE chrom3-contig1.pf SEQ-FILE chrom3-contig1.fsa // ID CONTIG-2 NAME Contig 2 of Chromosome 3 TYPE :CONTIG ANNOT-FILE chrom3-contig2.pf SEQ-FILE chrom3-contig2.fsa //