fids_to_dna_sequences allows the user to look up the DNA sequences corresponding to each of a set of fids.
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
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 fids_to_dna_sequences. It is documented as follows:
$return = $obj->fids_to_dna_sequences($fids)
$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
This is used only if the column containing the subsystem is not the last column.
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.
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.