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Robert Olson > Bio-KBase-0.06 > scripts/contigs_to_lengths


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contigs_to_lengths ^

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

    -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 contigs_to_lengths. It is documented as follows:

  $return = $obj->contigs_to_lengths($contigs)
Parameter and return types
$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

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 an extra column (the contig length) added.

Input lines that cannot be extended are written to stderr.

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