@gmod/gff/dist/util.d.ts

read and write GFF3 data as streams

/**
 * Unescape a string value used in a GFF3 attribute.
 *
 * @param stringVal - Escaped GFF3 string value
 * @returns An unescaped string value
 */
export declare function unescape(stringVal: string): string;
/**
 * Escape a value for use in a GFF3 attribute value.
 *
 * @param rawVal - Raw GFF3 attribute value
 * @returns An escaped string value
 */
export declare function escape(rawVal: string | number): string;
/**
 * Escape a value for use in a GFF3 column value.
 *
 * @param rawVal - Raw GFF3 column value
 * @returns An escaped column value
 */
export declare function escapeColumn(rawVal: string | number): string;
/**
 * Parse the 9th column (attributes) of a GFF3 feature line.
 *
 * @param attrString - String of GFF3 9th column
 * @returns Parsed attributes
 */
export declare function parseAttributes(attrString: string): GFF3Attributes;
/**
 * Parse a GFF3 feature line
 *
 * @param line - GFF3 feature line
 * @returns The parsed feature
 */
export declare function parseFeature(line: string): GFF3FeatureLine;
/**
 * Parse a GFF3 directive line.
 *
 * @param line - GFF3 directive line
 * @returns The parsed directive
 */
export declare function parseDirective(line: string): GFF3Directive | GFF3SequenceRegionDirective | GFF3GenomeBuildDirective | null;
/**
 * Format an attributes object into a string suitable for the 9th column of GFF3.
 *
 * @param attrs - Attributes
 * @returns GFF3 9th column string
 */
export declare function formatAttributes(attrs: GFF3Attributes): string;
/**
 * Format a feature object or array of feature objects into one or more lines of
 * GFF3.
 *
 * @param featureOrFeatures - A feature object or array of feature objects
 * @returns A string of one or more GFF3 lines
 */
export declare function formatFeature(featureOrFeatures: GFF3FeatureLine | GFF3FeatureLineWithRefs | (GFF3FeatureLine | GFF3FeatureLineWithRefs)[]): string;
/**
 * Format a directive into a line of GFF3.
 *
 * @param directive - A directive object
 * @returns A directive line string
 */
export declare function formatDirective(directive: GFF3Directive): string;
/**
 * Format a comment into a GFF3 comment.
 * Yes I know this is just adding a # and a newline.
 *
 * @param comment - A comment object
 * @returns A comment line string
 */
export declare function formatComment(comment: GFF3Comment): string;
/**
 * Format a sequence object as FASTA
 *
 * @param seq - A sequence object
 * @returns Formatted single FASTA sequence string
 */
export declare function formatSequence(seq: GFF3Sequence): string;
/**
 * Format a directive, comment, sequence, or feature, or array of such items,
 * into one or more lines of GFF3.
 *
 * @param itemOrItems - A comment, sequence, or feature, or array of such items
 * @returns A formatted string or array of strings
 */
export declare function formatItem(item: GFF3FeatureLineWithRefs | GFF3Directive | GFF3Comment | GFF3Sequence): string;
export declare function formatItem(items: (GFF3FeatureLineWithRefs | GFF3Directive | GFF3Comment | GFF3Sequence)[]): string[];
/** A record of GFF3 attribute identifiers and the values of those identifiers */
export type GFF3Attributes = Record<string, string[]>;
/** A representation of a single line of a GFF3 file */
export interface GFF3FeatureLine {
    /** The ID of the landmark used to establish the coordinate system for the current feature */
    seq_id: string | null;
    /** A free text qualifier intended to describe the algorithm or operating procedure that generated this feature */
    source: string | null;
    /** The type of the feature */
    type: string | null;
    /** The start coordinates of the feature */
    start: number | null;
    /** The end coordinates of the feature */
    end: number | null;
    /** The score of the feature */
    score: number | null;
    /** The strand of the feature */
    strand: string | null;
    /** For features of type "CDS", the phase indicates where the next codon begins relative to the 5' end of the current CDS feature */
    phase: string | null;
    /** Feature attributes */
    attributes: GFF3Attributes | null;
}
/**
 * A GFF3 Feature line that includes references to other features defined in
 * their "Parent" or "Derives_from" attributes
 */
export interface GFF3FeatureLineWithRefs extends GFF3FeatureLine {
    /** An array of child features */
    child_features: GFF3Feature[];
    /** An array of features derived from this feature */
    derived_features: GFF3Feature[];
}
/**
 * A GFF3 feature, which may include multiple individual feature lines
 */
export type GFF3Feature = GFF3FeatureLineWithRefs[];
/** A GFF3 directive */
export interface BaseGFF3Directive {
    /** The name of the directive */
    directive: string;
    /** The string value of the directive */
    value?: string;
}
/** A GFF3 sequence-region directive */
export interface GFF3SequenceRegionDirective extends BaseGFF3Directive {
    /** The string value of the directive */
    value: string;
    /** The sequence ID parsed from the directive */
    seq_id: string;
    /** The sequence start parsed from the directive */
    start: string;
    /** The sequence end parsed from the directive */
    end: string;
}
/** A GFF3 genome-build directive */
export interface GFF3GenomeBuildDirective extends BaseGFF3Directive {
    /** The string value of the directive */
    value: string;
    /** The genome build source parsed from the directive */
    source: string;
    /** The genome build name parsed from the directive */
    buildName: string;
}
export type GFF3Directive = BaseGFF3Directive | GFF3SequenceRegionDirective | GFF3GenomeBuildDirective;
/** A GFF3 comment */
export interface GFF3Comment {
    /** The text of the comment */
    comment: string;
}
/** A GFF3 FASTA single sequence */
export interface GFF3Sequence {
    /** The ID of the sequence */
    id: string;
    /** The description of the sequence */
    description?: string;
    /** The sequence */
    sequence: string;
}
export type GFF3Item = GFF3Feature | GFF3Directive | GFF3Comment | GFF3Sequence;