entrcmd1

Non-interactive command line interface for entrez

Usage

entrcmd [-] [-c] [-d str] [-e str] [-f] [-g F] [-h] [-i str] [-l str] [-n filename] [-o filename] -p str [-r] [-s] [-t str] [-u str] [-w str] [-x str] [-y N]

Overview

entrcmd is a non-interactive command-line interface which allows a user to perform a series of neighboring and output operations, based upon an initial set of UIDs or a boolean expression which describes a set of UIDs. Alternatively, it can be used to display an alphabetically sorted list of terms near an initial term.

Options

A summary of options is included below.

-: Print usage message

-c: 'Check' WWW output Forms

-d str: Initial database (default = m)

-e str: Boolean expression

-f: For WWW output, use Forms

-g F: Do not use WWW-style encoding for special input characters

-h: Print detailed help. Requires, but ignores, -p str

-i str: Comma-delimited list of files to import for named UID list

-l str: Taxonomy lookup string

-n filename: On-the-fly neighboring from filename

-o filename: Output file (default = stdout)

-p str: Program of commands

-r: Get sequences from ID Repository

-s: Display status report

-t str: Produce a list of terms

-u str: Comma-delimited list of UIDs

-w str: Produce WWW/HTML formatted output, using str (/htbin is recommended) as the directory prefix for linked hypertext items.

-x str: Name of export file for named UID list

-y N

Complexity:

1: bioseq only

2: bioseq set

3: nuc-prot set (default)

Releases

3 releases since Debian 3.0 (Woody); the text changed 1 time.