contigs_to_sequences

contigs_to_sequences is used to access the DNA sequence associated with each of a set of input contigs. It takes as input a set of contig IDs (from which the genome can be determined) and produces a mapping from the input IDs to the returned DNA sequence in each case.

Normally, people want to get back a fasta file, so that is the default (the input table is essentially discarded, keeping only the fasta file). The alternative to to add a column to the table (containing the contig sequence). The "-fasta=0" argument should be used, if you do not want fasta output.

Example:

contigs_to_sequences [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_sequences. It is documented as follows:

$return = $obj->contigs_to_sequences($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 dna
contigs is a reference to a list where each element is a contig
contig is a string
dna is a string

Command-Line Options

-c Column

This is used only if the column containing the contig IDs is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

-fasta

This is used to request a fasta output file (dropping all of the other columns in the input lines). It defaults to outputing just a fasta entry.

Output Format

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

Input lines that cannot be extended are written to stderr.