NAME

Smash::Utils::ACE - ACE assembly format file parser.

SYNOPSIS

        # create the object

        my $ace = new Smash::Utils::ACE("454Contigs.ace");

        print $ace->contigs."\n";
        print $ace->reads."\n";

        # process each contig

        while (my $contig = $ace->nextContig) {
                printf ">%s\n", $contig->name;
                printf Smash::Core->pretty_fasta($contig->sequence);
        }

DESCRIPTION

Member variables

file
source
contigs
reads

Member functions

_parse_header(): parses the ACE header
nextContig(): returns the next contig in the ACE file as a Smash::Utils::ACE::Contig object.
getNextLine(): reads the next non-empty line and stores it in LAST_LINE.
getSequence(): gets the sequence in the ACE file (sequence continues until the next empty line in ACE format)

NAME

Smash::Utils::ACE::Contig - Class to hold a contig from the ACE file.

SYNOPSIS

        my $contig = Smash::Utils::ACE::Contig->new( \
                                NAME => $name, \
                                PADDED_LENGTH => $length, \
                                READS => $reads, \
                                DIR => $dir\
                        );

        # print the unpadded contig sequence in fasta format

        printf ">%s\n%s", $contig->name, Smash::Core->pretty_fasta($contig->sequence);