;;========================================================================== ;; Sample genetic-elements.dat file, created 2/13/2001 by Suzanne Paley. ;; PathoLogic v. 1.8 ;; ;; 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 either with a single annotation file or as a set ;; of contigs (but not both). Contigs are each described with a single ;; annotation file. Records are ended by a single line containing only the ;; string "//". 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. Unique 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. Case insensitive. ;; NAME -- Optional. Descriptive name for the genetic element ;; TYPE -- Optional. One of :CHRSM, :PLASMID, :MT (mitochondrial chromosome), ;; :PT (chloroplast chromosome), or :CONTIG. Defaults to :CHRSM. ;; CIRCULAR? -- Required (except for contigs). Is the genetic element ;; circular? Valid options are 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 annotations file for this genetic element. The file ;; must be in either pathologic format (.pf) or genbank ;; format (.gbk). If the file is in the orgcyc/version/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 ;; (.fna or .fsa). If the file is in the orgcyc/version/input/ ;; directory, then only the filename is required, otherwise a full ;; pathname must be supplied. ;; CONTIG -- Optional (for all types other than :CONTIG. This field is 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. ;; ;; Note that the "//" is required after the final genetic element, also. ;;=========================================================================== ID TEST-CHROM-1 NAME Chromosome 1 TYPE :CHRSM CIRCULAR? N ANNOT-FILE chrom1.pf SEQ-FILE chrom1.fsa // ID TEST-CHROM-2 NAME Chromosome 2 CIRCULAR? N ANNOT-FILE /mydata/chrom2.gbk SEQ-FILE /mydata/chrom2.fna // ID TEST-CHROM-3 NAME Chromosome 3 TYPE :CHRSM CIRCULAR? N CONTIG CONTIG-1 CONTIG CONTIG-2 // ID TEST-MIT-CHROM NAME Mitochondrial chromosome TYPE :MT CIRCULAR? Y CODON-TABLE 2 ANNOT-FILE mit-chrom.pf // 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 //