fids_to_dna_sequences

fids_to_dna_sequences allows the user to look up the DNA sequences corresponding to each of a set of fids.

Example:

    fids_to_dna_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 fids_to_dna_sequences. It is documented as follows:

  $return = $obj->fids_to_dna_sequences($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 dna_sequence
fids is a reference to a list where each element is a fid
fid is a string
dna_sequence is a string

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 ]

-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 just a fasta file with the sequence. You can also get a tab-delimited file by using -fasta=0. The tab-delimited format consists of the input file with an extra column of sequence added.

Input lines that cannot be extended are written to stderr.