This method creates a pseudo-FIG object for use by the FullLocation object. It supports the contig_ln and dna_seq methods.
Note that it keeps all the data structures in memory, so it should not be used except for a few genomes with small number of gen
my $cdna = ContigDNA->new($genID1 => $file1, $genID2 => $file, ... $genIDN => $fileN );
Construct a new pseudo-FIG object from a set of FASTA files. The incoming parameters come in pairs. The first of each pair is the ID of a genome; the second is the name of a FASTA file containing the contig data.
IDs of the genomes whose contigs are to be read into memory.
Names of the FASTA files containing the genome data.
my $sequence = $sfxlate->dna_seq($genomeID, @locations);
Return the sequence represented by a list of locations. The locations
should be in the standard form contigID_begindirend.
ID of the relevant genome.
List of locations to be included in the DNA sequence.
Returns a string specifying the DNA nucleotides in the specified locations.
my $length = $sfxlate->contig_ln($genomeID, $contig);
Return the length of the specified contig.
ID of the genome to which the contig belongs.
ID of the contig whose length is desired.
Returns the length (in base pairs) of the specified contig in the specified genome.