fids_to_feature_data

Example:

fids_to_feature_data [arguments] < input > output

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the identifer. If another column contains the identifier use

-c N

where N is the column (from 1) that contains the subsystem.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Documentation for underlying call

This script is a wrapper for the CDMI-API call fids_to_feature_data. It is documented as follows:

$return = $obj->fids_to_feature_data($fids)

Parameter and return types

$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a feature_data
fids is a reference to a list where each element is a fid
fid is a string
feature_data is a reference to a hash where the following keys are defined:
	feature_id has a value which is a fid
	genome_name has a value which is a string
	feature_function has a value which is a string
	feature_length has a value which is an int
	feature_publications has a value which is a pubrefs
	feature_location has a value which is a location
pubrefs is a reference to a list where each element is a pubref
pubref is a reference to a list containing 3 items:
	0: a string
	1: a string
	2: a string
location is a reference to a list where each element is a region_of_dna
region_of_dna is a reference to a list containing 4 items:
	0: a contig
	1: a begin
	2: a strand
	3: a length
contig is a string
begin is an int
strand is a string
length is an int

Command-Line Options

-c Column

This is used only if the column containing the subsystem is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with extra columns added in this order:

feature_id

Feature identifier

feature_publications

List of Pubmed identifiers for publications associated with this feature.

genome_name

Name of the genome this feature is present in.

feature_location

Location string describing the location of this feature in its genome.

feature_length

Length of the DNA sequence of this feature.

feature_function

The function currently assigned to this feature.

Input lines that cannot be extended are written to stderr.