In some cases, one wishes to know just the lengths of the contigs, rather than their actual DNA sequence (e.g., suppose that you wished to know if a gene boundary occured within 100 bp of the end of the contig). To avoid requiring a user to access the entire DNA sequence, we offer the ability to retrieve just the contig lengths. Input to the routine is a list of contig IDs. The routine returns a mapping from contig IDs to lengths
contigs_to_lengths [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
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.
This script is a wrapper for the CDMI-API call contigs_to_lengths. It is documented as follows:
$return = $obj->contigs_to_lengths($contigs)
$contigs is a contigs $return is a reference to a hash where the key is a contig and the value is a length contigs is a reference to a list where each element is a contig contig is a string length is an int
This is used only if the column containing the subsystem is not the last column.
The standard output is a tab-delimited file. It consists of the input file with an extra column (the contig length) added.
Input lines that cannot be extended are written to stderr.